Canonical, grand-canonical and isothermal/isobaric ensemble Monte Carlo simulations and their analysis
=== Mihaly Mezei ===
Computer word size: 32 bits Largest real and double= 0.70E+38 0.10+301 Number of bits per word in a bitmap= 31
Maximum number of atoms=21996, solvents+1=3000, solute atoms=10000, solvent atoms/molecule=4
Program was last modified on 07/19/1010, simulation and proximity common blocks were last modified on 07/09/2010 and 02/12/2009, resp.
Date: Tue Jul 20 05:11:54 2010
Unix hostname: atlas.physbio.mssm.edu
Unix directory: /hosts/atlas/homes/mezei/.www/mmc/examples
MMC> Input line 1 : FILE f8
MMC> Input line 2 : PRNT ECHO
MMC> Input line 3 : TITL 1tf_8_13
MMC> Input line 4 : NSLV 0
Integer number read: 0
Integer default set to 0
MMC> Input line 5 : TEMP 298.0
Real number read: 298.000000
MMC> Input line 6 : SVVC SPCC 9.05 ! Solvent cutoff
Real number read: 9.050000
Real default set to 0.000000
Real default set to 0.000000
Real default set to 0.000000
Real default set to 0.000000
MMC> Input line 7 : SUVC SPCC 12.0
Real number read: 12.000000
MMC> Input line 8 : PBCN RECT 70.0 70.0 70.0
Real number read: 70.000000
Real number read: 70.000000
Real number read: 70.000000
MMC> Input line 9 : STEP 0.00 00.0 0.55 40.0 30
Real number read: 0.000000
Real number read: 0.000000
Real number read: 0.550000
Real number read: 40.000000
Integer number read: 30
MMC> Input line 10 : SUPT CHRM
Default key set: CLMG
MMC> Input line 11 : SAMP METC 0.5 ! Scaled force-biased sampling
MMC> Input line 12 : MOVE RAND
MMC> Input line 13 : SVPT TIP3 TIP3 ! Solvent-solvent potential is TIP4P
MMC> Input line 14 : SLTA SMPL PDB FILE 3928
Integer number read: 3928
Integer default set to 0
Integer default set to 0
Integer default set to 3928
Integer default set to 1
+++++ FORMATTED file f8.pdb as unit 10, Mode=OLD, type=15 has been opened
>>>>> OVERRIDE: non-MMC solute input has no potential type information - SUPT CHRM is changed to SUPT ATNO
>>>>> OVERRIDE: PDB file only contained 1989 atoms
----- WARNING: atom 47 (LEU CG ), atomic no= 6 has 5 neighbours:
Atom 46 (LEU CB ) Distance= 1.523 Threshold= 1.650 Atom 48 (LEU CD1) Distance= 1.493 Threshold= 1.650
Atom 49 (LEU CD1) Distance= 1.500 Threshold= 1.650 Atom 50 (LEU CD2) Distance= 1.505 Threshold= 1.650
Atom 51 (LEU CD2) Distance= 1.539 Threshold= 1.650 Atom
----- WARNING: atom 397 (LEU CG ), atomic no= 6 has 5 neighbours:
Atom 396 (LEU CB ) Distance= 1.536 Threshold= 1.650 Atom 398 (LEU CD1) Distance= 1.530 Threshold= 1.650
Atom 399 (LEU CD1) Distance= 1.513 Threshold= 1.650 Atom 400 (LEU CD2) Distance= 1.523 Threshold= 1.650
Atom 401 (LEU CD2) Distance= 1.505 Threshold= 1.650 Atom
----- WARNING: atom 1457 (GLN CD ), atomic no= 6 has 6 neighbours:
Atom 1455 (GLN CG ) Distance= 1.511 Threshold= 1.650 Atom 1456 (GLN CG ) Distance= 1.591 Threshold= 1.650
Atom 1458 (GLN CD ) Distance= 0.615 Threshold= 1.650 Atom 1459 (GLN OE1) Distance= 1.229 Threshold= 1.700
Atom 1461 (GLN NE2) Distance= 1.337 Threshold= 1.700 Atom 1462 (GLN NE2) Distance= 0.848 Threshold= 1.700
----- WARNING: atom 1458 (GLN CD ), atomic no= 6 has 6 neighbours:
Atom 1455 (GLN CG ) Distance= 1.215 Threshold= 1.650 Atom 1456 (GLN CG ) Distance= 1.500 Threshold= 1.650
Atom 1457 (GLN CD ) Distance= 0.615 Threshold= 1.650 Atom 1460 (GLN OE1) Distance= 1.232 Threshold= 1.700
Atom 1461 (GLN NE2) Distance= 1.379 Threshold= 1.700 Atom 1462 (GLN NE2) Distance= 1.327 Threshold= 1.700
----- WARNING short bond between atoms 721 (LYS CE ) and 722 (LYS CE ) r= 0.63 A
----- WARNING short bond between atoms 722 (LYS CE ) and 721 (LYS CE ) r= 0.63 A
----- WARNING short bond between atoms 1457 (GLN CD ) and 1458 (GLN CD ) r= 0.62 A
----- WARNING short bond between atoms 1458 (GLN CD ) and 1457 (GLN CD ) r= 0.62 A
Number of different atom types found in the solute= 4
+++++ Closing unit 10
MMC> Input line 15 : GCEN CAVB RSIG ! Grand-canonical ensemble, cavity biased,
>>>>> OVERRIDE: solute radius source is set to VdW since no potential information was read
Default key set: ALTI
Default key set: ALLG
Default key set: LJQI
rectype 13 : 2.00000 2.50000 1000.00 250 250 250 1000 1 1 10000 20000
===== STRONG WARNING: Cavity grid shift frequency is too low, resulting in excess CPU time. Increase it to 50000 or more
MMC> Input line 17 : CNFG READ PDB
Default key set: NOFX
Integer default set to 0
+++++ FORMATTED file f8.pdb as unit 10, Mode=OLD, type=15 has been opened
MMC> Input line 18 : PRTG PDB ALLG AGLS 0 0 0.8 10.0 0.2 1.0 0.5 0.0 1 3 0 0
Integer default set to 1
Integer default set to 0
Real number read: 0.800000
Real number read: 10.000000
Real number read: 0.200000
Real number read: 1.000000
Real number read: 0.500000
Real default set to 0.000000
Integer number read: 1
Integer number read: 3
Integer default set to 0
Integer default set to 1
+++++ Closing unit 10
Initializing the covering grid with a shift of 0.500 0.500 0.500 A
Using Rcav= 2.50 A, the solute covers 4541067 gridpoints, leaving 11083933 gridpoints
=== Calculation of cavities and pockets based on a 250x250x250 grid and probe radius of 2.50 A ===
Grid intervals in the x, y, and z directions: 0.16 0.21 0.28 A
Writing cavity grid file in PDB format
No unfiltered external gridpoints will be written out
Minimum number of gridpoints in a printed cavity= 21 (minimum volume= 0.20 A**3)
All cavity gridpoints will be written out
External gridpoints will also be filtered by circular variance (to detect pockets):
Gridpoints with CV < 0.800 will be dropped (cutoff= 10.00 A)
Minimum number of gridpoints in a printed pocket= 108 (minimum volume= 1.00 A**3)
File f8_2.pdb is already present
File f8_3.pdb is already present
File f8_4.pdb is already present
File f8_5.pdb is already present
File f8_6.pdb is already present
File f8_7.pdb is already present
+++++ FORMATTED file f8_8.pdb as unit 10, Mode=NEW, type=15 has been opened
Cavity 0 residue 260 resname=CAV chainid=G # of grids= 198 volume estimate= 1.82 A**3 Formal charge= 0.0
Cavity contact residues: 60 ILE 125 LEU 126 ALA 129 ILE 151 LEU 155 LEU
Cavity contact atoms: 972 C LEU 973 O LEU 975 CG LEU 978 N ALA 979 CA ALA 1008 CB ILE
1009 CG1 ILE 1011 CD1 ILE 1179 CD1 LEU 1209 CD2 LEU 977 CD2 LEU 1208 CD1 LEU 1207 CG LEU 477 CD1 ILE
1178 CG LEU 476 CG2 ILE
Cavity 1 residue 261 resname=CAV chainid=G # of grids= 189 volume estimate= 1.74 A**3 Formal charge= 1.0
Cavity contact residues: 23 LEU 26 TYR 28 LEU 252 ALA 256 ARG
Cavity contact atoms: 208 CD1 TYR 1927 O ALA 1928 CB ALA 1953 CG ARG 1954 CD ARG 189 CD2 LEU
225 CD2 LEU 1925 CA ALA 183 CA LEU 185 O LEU 184 C LEU 206 CB TYR 207 CG TYR 1926 C ALA
176 O GLU
Cavity 2 residue 262 resname=CAV chainid=G # of grids= 48 volume estimate= 0.44 A**3 Formal charge= 0.0
Cavity contact residues: 62 THR 99 VAL 122 ALA 125 LEU 151 LEU
Cavity contact atoms: 948 CA ALA 949 C ALA 950 O ALA 974 CB LEU 977 CD2 LEU 1180 CD2 LEU
799 CG2 VAL 495 CG2 THR 951 CB ALA
Cavity 3 residue 263 resname=CAV chainid=G # of grids= 103 volume estimate= 0.95 A**3 Formal charge= 0.0
Cavity contact residues: 60 ILE 61 PHE 62 THR 97 TYR 98 VAL 99 VAL 125 LEU
Cavity contact atoms: 786 N VAL 787 CA VAL 788 C VAL 793 N VAL 799 CG2 VAL 977 CD2 LEU
481 O PHE 476 CG2 ILE 495 CG2 THR 480 C PHE 777 O TYR 776 C TYR 478 N PHE
Cavity 4 residue 264 resname=CAV chainid=G # of grids= 753 volume estimate= 6.92 A**3 Formal charge= -1.0
Cavity contact residues: 5 LEU 19 TYR 22 GLU 23 LEU 248 PRO 251 LEU 252 ALA
Cavity contact atoms: 177 CB GLU 178 CG GLU 1898 O PRO 1928 CB ALA 182 N LEU 145 O TYR
187 CG LEU 188 CD1 LEU 1923 CD2 LEU 146 CB TYR 40 CD1 LEU 41 CD2 LEU 144 C TYR 143 CA TYR
149 CD2 TYR 1921 CG LEU 1920 CB LEU 189 CD2 LEU 1947 CD1 ILE 1924 N ALA 147 CG TYR 175 C GLU
1896 CA PRO 1897 C PRO 1918 C LEU 1925 CA ALA 1899 CB PRO 1919 O LEU
Cavity 5 residue 265 resname=CAV chainid=G # of grids= 475 volume estimate= 4.36 A**3 Formal charge= 1.0
Cavity contact residues: 58 GLY 59 LEU 91 TRP 94 LYS 95 SER 96 VAL 112 LEU
Cavity contact atoms: 728 O TRP 754 C LYS 756 CB LYS 761 N SER 763 C SER 764 O SER
773 CG2 VAL 735 CE3 TRP 459 CA GLY 462 N LEU 460 C GLY 466 CB LEU 467 CG LEU 468 CD1 LEU
729 CB TRP 726 CA TRP 727 C TRP 883 CD1 LEU 884 CD2 LEU
Cavity 6 residue 266 resname=CAV chainid=G # of grids= 21 volume estimate= 0.19 A**3 Formal charge= 0.0
Cavity contact residues: 61 PHE 96 VAL 97 TYR 98 VAL 107 VAL
Cavity contact atoms: 772 CG1 VAL 792 CG2 VAL 848 CG1 VAL 849 CG2 VAL 484 CD1 PHE 777 O TYR
776 C TYR
Cavity 7 residue 267 resname=CAV chainid=G # of grids= 25 volume estimate= 0.23 A**3 Formal charge= 0.0
Cavity contact residues: 59 LEU 97 TYR 139 LEU
Cavity contact atoms: 462 N LEU 464 C LEU 465 O LEU 475 CG1 ILE 780 CD1 TYR 1083 CD2 LEU
460 C GLY 463 CA LEU 1080 CB LEU 470 N ILE 1081 CG LEU 461 O GLY 782 CE1 TYR
Cavity 8 residue 268 resname=CAV chainid=G # of grids= 23 volume estimate= 0.21 A**3 Formal charge= 0.0
Cavity contact residues: 59 LEU 61 PHE 96 VAL 97 TYR
Cavity contact atoms: 484 CD1 PHE 772 CG1 VAL 777 O TYR 465 O LEU 464 C LEU 478 N PHE
470 N ILE 466 CB LEU 486 CE1 PHE 774 N TYR 471 CA ILE 472 C ILE
Cavity 9 residue 269 resname=CAV chainid=G # of grids= 144 volume estimate= 1.32 A**3 Formal charge= 0.0
Cavity contact residues: 60 ILE 141 PHE 151 LEU 155 LEU
Cavity contact atoms: 477 CD1 ILE 1177 CB LEU 1178 CG LEU 1179 CD1 LEU 1208 CD1 LEU 1259 SD MET
1097 CG PHE 1099 CD2 PHE 1101 CE2 PHE 1260 CE MET 1098 CD1 PHE 476 CG2 ILE 1102 CZ PHE 1100 CE1 PHE
474 CB ILE
Cavity 10 residue 270 resname=CAV chainid=G # of grids= 24 volume estimate= 0.22 A**3 Formal charge= 0.0
Cavity contact residues: 139 LEU 155 LEU 161 ALA 162 MET
Cavity contact atoms: 1082 CD1 LEU 1208 CD1 LEU 1246 CG2 ILE 1251 O ALA 1257 CB MET 1081 CG LEU
1080 CB LEU 1258 CG MET 1259 SD MET
Cavity 11 residue 271 resname=CAV chainid=G # of grids= 1400 volume estimate= 12.86 A**3 Formal charge= 1.0
Cavity contact residues: 192 SER 220 LYS 221 PHE 222 ALA 240 SER 241 CYS 255 ILE 258 ALA 259 LEU
Cavity contact atoms: 1852 CB CYS 1939 O GLY 1941 CA ILE 1972 CB ALA 1491 OG SER 1708 O LYS
1709 CB LYS 1707 C LYS 1729 CB ALA 1716 C PHE 1717 O PHE 1725 N ALA 1726 CA ALA 1846 CB SER
1490 CB SER 1980 CD2 LEU 1710 CG LYS 1978 CG LEU 1945 CG1 ILE 1946 CG2 ILE 1848 N CYS 1853 SG CYS
1844 C SER 1944 CB ILE 1979 CD1 LEU 1970 C ALA 1943 O ILE 1942 C ILE 1973 N LEU
Cavity 12 residue 272 resname=CAV chainid=G # of grids= 297 volume estimate= 2.73 A**3 Formal charge= 0.0
Cavity contact residues: 61 PHE 67 VAL 107 VAL 110 ILE 112 LEU
Cavity contact atoms: 844 CA VAL 845 C VAL 846 O VAL 848 CG1 VAL 870 CG1 ILE 883 CD1 LEU
882 CG LEU 872 CD1 ILE 486 CE1 PHE 488 CZ PHE 881 CB LEU 847 CB VAL 530 CG1 VAL 484 CD1 PHE
849 CG2 VAL 531 CG2 VAL
Cavity 13 residue 273 resname=CAV chainid=G # of grids= 125 volume estimate= 1.15 A**3 Formal charge= 1.0
Cavity contact residues: 53 PRO 56 TYR 58 GLY 91 TRP 94 LYS
Cavity contact atoms: 458 N GLY 459 CA GLY 735 CE3 TRP 737 CZ3 TRP 756 CB LYS 757 CG LYS
758 CD LYS 445 O TYR 444 C TYR 446 CB TYR 421 O PRO 738 CH2 TRP 456 C GLY 759 CE LYS
419 CA PRO 422 CB PRO 420 C PRO 732 CD2 TRP
Cavity 14 residue 274 resname=CAV chainid=G # of grids= 52 volume estimate= 0.48 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 23 LEU 28 LEU 255 ILE
Cavity contact atoms: 24 CG1 VAL 189 CD2 LEU 223 CG LEU 225 CD2 LEU 1946 CG2 ILE 25 CG2 VAL
23 CB VAL 1947 CD1 ILE 188 CD1 LEU 222 CB LEU 186 CB LEU 187 CG LEU
Cavity 15 residue 275 resname=CAV chainid=G # of grids= 38 volume estimate= 0.35 A**3 Formal charge= 0.0
Cavity contact residues: 60 ILE 139 LEU 140 LEU 141 PHE
Cavity contact atoms: 475 CG1 ILE 477 CD1 ILE 1078 C LEU 1080 CB LEU 1084 N LEU 1086 C LEU
1087 O LEU 1079 O LEU 1096 CB PHE 1092 N PHE 1093 CA PHE 1258 CG MET 1259 SD MET 474 CB ILE
Cavity 16 residue 276 resname=CAV chainid=G # of grids= 37 volume estimate= 0.34 A**3 Formal charge= 0.0
Cavity contact residues: 59 LEU 60 ILE 61 PHE 142 PRO
Cavity contact atoms: 464 C LEU 466 CB LEU 469 CD2 LEU 470 N ILE 472 C ILE 473 O ILE
483 CG PHE 484 CD1 PHE 486 CE1 PHE 488 CZ PHE 1109 CD PRO 487 CE2 PHE 1108 CG PRO 485 CD2 PHE
467 CG LEU
Cavity 17 residue 277 resname=CAV chainid=G # of grids= 277 volume estimate= 2.54 A**3 Formal charge= 0.0
Cavity contact residues: 221 PHE 222 ALA 223 ALA 232 LEU 237 LEU 238 PRO 239 VAL
Cavity contact atoms: 1716 C PHE 1717 O PHE 1725 N ALA 1726 CA ALA 1727 C ALA 1730 N ALA
1840 CG1 VAL 1851 O CYS 1795 CD1 LEU 1718 CB PHE 1836 CA VAL 1831 O PRO 1796 CD2 LEU 1794 CG LEU
1824 CB LEU 1841 CG2 VAL 1839 CB VAL 1793 CB LEU 1823 O LEU 1822 C LEU 1830 C PRO 1835 N VAL
1734 CB ALA
Cavity 18 residue 278 resname=CAV chainid=G # of grids= 501 volume estimate= 4.60 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 4 LEU 5 LEU 23 LEU 192 SER 194 THR 255 ILE
Cavity contact atoms: 25 CG2 VAL 41 CD2 LEU 188 CD1 LEU 1947 CD1 ILE 23 CB VAL 29 O LEU
26 N LEU 28 C LEU 21 C VAL 34 N LEU 1489 O SER 1488 C SER 1491 OG SER 1492 N ILE
1493 CA ILE 1500 N THR 1494 C ILE 1505 OG1 THR 1490 CB SER 24 CG1 VAL 1946 CG2 ILE 1945 CG1 ILE
Cavity 19 residue 279 resname=CAV chainid=G # of grids= 30 volume estimate= 0.28 A**3 Formal charge= 0.0
Cavity contact residues: 1 MET 3 VAL 28 LEU 259 LEU
Cavity contact atoms: 4 O MET 5 CB MET 223 CG LEU 224 CD1 LEU 1979 CD1 LEU 3 C MET
24 CG1 VAL
Cavity 20 residue 280 resname=CAV chainid=G # of grids= 197 volume estimate= 1.81 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 4 LEU 5 LEU 20 ILE 30 ALA 31 THR 32 LEU
Cavity contact atoms: 40 CD1 LEU 155 CA ILE 158 CB ILE 160 CG2 ILE 239 CB ALA 237 C ALA
240 N THR 241 CA THR 242 C THR 243 O THR 247 N LEU 39 CG LEU 38 CB LEU 248 CA LEU
251 CB LEU 22 O VAL 34 N LEU 28 C LEU 21 C VAL 27 CA LEU 238 O ALA 236 CA ALA
25 CG2 VAL 26 N LEU 41 CD2 LEU
Cavity 21 residue 281 resname=CAV chainid=G # of grids= 24 volume estimate= 0.22 A**3 Formal charge= 0.0
Cavity contact residues: 50 LEU 59 LEU 83 TRP 91 TRP
Cavity contact atoms: 399 CD1 LEU 468 CD1 LEU 660 CZ3 TRP 661 CH2 TRP 730 CG TRP 731 CD1 TRP
732 CD2 TRP 400 CD2 LEU 733 NE1 TRP 734 CE2 TRP
Cavity 22 residue 282 resname=CAV chainid=G # of grids= 21 volume estimate= 0.19 A**3 Formal charge= 1.0
Cavity contact residues: 1 MET 2 LYS 3 VAL 191 ALA 259 LEU
Cavity contact atoms: 5 CB MET 24 CG1 VAL 1485 CB ALA 1979 CD1 LEU 3 C MET 12 O LYS
11 C LYS 9 N LYS 4 O MET
Cavity 23 residue 283 resname=CAV chainid=G # of grids= 371 volume estimate= 3.41 A**3 Formal charge= 0.0
Cavity contact residues: 195 PHE 197 SER 198 PRO 201 LEU 228 THR 231 ALA 232 LEU
Cavity contact atoms: 1535 N PRO 1536 CA PRO 1762 CA THR 1764 O THR 1767 CG2 THR 1788 CB ALA
1532 O SER 1556 CB LEU 1559 CD2 LEU 1531 C SER 1763 C THR 1557 CG LEU 1511 CB PHE 1794 CG LEU
1558 CD1 LEU 1512 CG PHE 1513 CD1 PHE 1789 N LEU 1796 CD2 LEU 1795 CD1 LEU
Cavity 24 residue 284 resname=CAV chainid=G # of grids= 33 volume estimate= 0.30 A**3 Formal charge= 0.0
Cavity contact residues: 193 ILE 195 PHE 221 PHE 222 ALA 232 LEU
Cavity contact atoms: 1716 C PHE 1718 CB PHE 1725 N ALA 1728 O ALA 1795 CD1 LEU 1513 CD1 PHE
1515 CE1 PHE 1721 CD2 PHE 1719 CG PHE 1796 CD2 LEU 1495 O ILE 1715 CA PHE
Cavity 25 residue 285 resname=CAV chainid=G # of grids= 54 volume estimate= 0.50 A**3 Formal charge= -1.0
Cavity contact residues: 141 PHE 143 CYS 146 LEU 149 GLU 152 PRO 164 SER
Cavity contact atoms: 1101 CE2 PHE 1160 CB GLU 1161 CG GLU 1186 CG PRO 1115 SG CYS 1135 CD2 LEU
1275 OG SER 1274 CB SER 1099 CD2 PHE
Cavity 26 residue 286 resname=CAV chainid=G # of grids= 143 volume estimate= 1.31 A**3 Formal charge= -1.0
Cavity contact residues: 8 ASP 35 VAL 36 LEU 197 SER 199 SER 200 GLY 203 TYR
Cavity contact atoms: 67 OD1 ASP 283 CD1 LEU 1534 OG SER 1546 CB SER 282 CG LEU 284 CD2 LEU
1548 N GLY 1544 C SER 1549 CA GLY 276 CG2 VAL 1573 CD1 TYR 1575 CE1 TYR 1545 O SER
Cavity 27 residue 287 resname=CAV chainid=G # of grids= 547 volume estimate= 5.02 A**3 Formal charge= 0.0
Cavity contact residues: 195 PHE 201 LEU 205 LEU 208 ILE 216 ILE 221 PHE 232 LEU 237 LEU
Cavity contact atoms: 1719 CG PHE 1720 CD1 PHE 1721 CD2 PHE 1796 CD2 LEU 1824 CB LEU 1825 CG LEU
1723 CE2 PHE 1724 CZ PHE 1591 CD1 LEU 1826 CD1 LEU 1679 CD1 ILE 1515 CE1 PHE 1517 CZ PHE 1558 CD1 LEU
1827 CD2 LEU 1619 CD1 ILE 1616 CB ILE 1618 CG2 ILE 1722 CE1 PHE
Cavity 28 residue 288 resname=CAV chainid=G # of grids= 58 volume estimate= 0.53 A**3 Formal charge= 1.0
Cavity contact residues: 46 PHE 49 LYS 140 LEU 165 ILE
Cavity contact atoms: 363 CD1 PHE 365 CE1 PHE 1089 CG LEU 1090 CD1 LEU 1091 CD2 LEU 1282 CG2 ILE
389 CD LYS 387 CB LYS 388 CG LYS 1283 CD1 ILE 358 CA PHE
Cavity 29 residue 289 resname=CAV chainid=G # of grids= 33 volume estimate= 0.30 A**3 Formal charge= 1.0
Cavity contact residues: 40 PHE 65 ARG 69 ALA 167 VAL 168 TYR
Cavity contact atoms: 511 C ARG 512 O ARG 520 N ALA 521 CA ALA 545 CB ALA 1297 CG2 VAL
1305 CD2 TYR 1302 CB TYR 1293 C VAL 1294 O VAL 1298 N TYR 318 CD2 PHE 320 CE2 PHE 1303 CG TYR
Cavity 30 residue 290 resname=CAV chainid=G # of grids= 87 volume estimate= 0.80 A**3 Formal charge= 0.0
Cavity contact residues: 38 PHE 39 GLU 40 PHE 65 ARG 168 TYR
Cavity contact atoms: 295 CB PHE 296 CG PHE 513 CB ARG 514 CG ARG 515 CD ARG 1303 CG TYR
1304 CD1 TYR 297 CD1 PHE 1302 CB TYR 305 O GLU 320 CE2 PHE 318 CD2 PHE 304 C GLU 321 CZ PHE
299 CE1 PHE
Cavity 31 residue 291 resname=CAV chainid=G # of grids= 36 volume estimate= 0.33 A**3 Formal charge= 0.0
Cavity contact residues: 4 LEU 6 LEU 33 ILE 180 LEU
Cavity contact atoms: 31 CG LEU 32 CD1 LEU 47 CG LEU 48 CD1 LEU 51 CD2 LEU 259 CB ILE
262 CD1 ILE 260 CG1 ILE 1395 CD2 LEU 33 CD2 LEU
Cavity 32 residue 292 resname=CAV chainid=G # of grids= 134 volume estimate= 1.23 A**3 Formal charge= 0.0
Cavity contact residues: 4 LEU 6 LEU 180 LEU 184 TYR 193 ILE 208 ILE
Cavity contact atoms: 33 CD2 LEU 48 CD1 LEU 49 CD1 LEU 1499 CD1 ILE 1619 CD1 ILE 1617 CG1 ILE
1395 CD2 LEU 50 CD2 LEU 1430 CE1 TYR 1433 OH TYR 1432 CZ TYR
Cavity 33 residue 293 resname=CAV chainid=G # of grids= 22 volume estimate= 0.20 A**3 Formal charge= 0.0
Cavity contact residues: 35 VAL 176 ILE 200 GLY 203 TYR 204 SER
Cavity contact atoms: 274 CB VAL 275 CG1 VAL 1551 O GLY 1571 CB TYR 1366 CD1 ILE 1583 CB SER
1569 C TYR 1579 N SER 1570 O TYR
Cavity 34 residue 294 resname=CAV chainid=G # of grids= 102 volume estimate= 0.94 A**3 Formal charge= 0.0
Cavity contact residues: 6 LEU 33 ILE 34 PRO 35 VAL 176 ILE 180 LEU
Cavity contact atoms: 51 CD2 LEU 261 CG2 ILE 266 O PRO 275 CG1 VAL 1364 CG1 ILE 1365 CG2 ILE
1363 CB ILE 265 C PRO 1366 CD1 ILE 1583 CB SER 1393 CG LEU 1394 CD1 LEU 1362 O ILE
Cavity 35 residue 295 resname=CAV chainid=G # of grids= 76 volume estimate= 0.70 A**3 Formal charge= 0.0
Cavity contact residues: 4 LEU 33 ILE 180 LEU 183 TYR 184 TYR
Cavity contact atoms: 33 CD2 LEU 262 CD1 ILE 1414 CB TYR 1415 CG TYR 1417 CD2 TYR 1395 CD2 LEU
1389 CA LEU 1391 O LEU 1428 CD1 TYR 1390 C LEU 1430 CE1 TYR
Cavity 36 residue 296 resname=CAV chainid=G # of grids= 25 volume estimate= 0.23 A**3 Formal charge= 0.0
Cavity contact residues: 189 VAL 212 SER 215 ASN
Cavity contact atoms: 1472 CG1 VAL 1650 CB SER 1666 C ASN 1667 O ASN 1668 CB ASN 1672 N ILE
1704 CD1 ILE 1647 CA SER 1649 O SER 1648 C SER 1473 CG2 VAL 1651 OG SER
Cavity 37 residue 297 resname=CAV chainid=G # of grids= 145 volume estimate= 1.33 A**3 Formal charge= 0.0
Cavity contact residues: 33 ILE 34 PRO 173 HIS 176 ILE 179 ASN
Cavity contact atoms: 261 CG2 ILE 263 N PRO 266 O PRO 268 CG PRO 269 CD PRO 1387 ND2 ASN
1344 ND1 HIS 1359 N ILE 1357 C GLY 1346 CE1 HIS 1360 CA ILE 1364 CG1 ILE 1343 CG HIS 1342 CB HIS
1358 O GLY
Cavity 38 residue 298 resname=CAV chainid=G # of grids= 123 volume estimate= 1.13 A**3 Formal charge= 0.0
Cavity contact residues: 180 LEU 184 TYR 207 HIS 208 ILE 211 LEU
Cavity contact atoms: 1395 CD2 LEU 1430 CE1 TYR 1617 CG1 ILE 1644 CD1 LEU 1392 CB LEU 1613 CA ILE
1394 CD1 LEU 1605 O HIS 1604 C HIS 1612 N ILE 1393 CG LEU 1642 CB LEU 1432 CZ TYR 1433 OH TYR
1615 O ILE 1614 C ILE
A total of 6991 cavity gridpoints were written to file f8_8.pdb
Residue number of the first cavity= 261
Attempting to find subclusters by shaving 1 layers off each cluster
Grids with 3, or less neighbors will be considered surface grids and will be shaved off
Grids shaved off as surface grids will be put back to the subcluster they were shaved off from
Cavity 17 original number of gridpoints= 198 number of gridpoints left after shaving= 104
Number of subclusters= 99 number of subclusters dropped= 94
Cavity 17 subcluster 1 residue= 6992 resname=CAV chainid=S
reduced number of grids= 41 corrected number of grids= 66 volume estimate= 0.61 A**3 Formal charge= 0.0
Cavity contact residues: 125 LEU 126 ALA 129 ILE 151 LEU 155 LEU
Cavity contact atoms: 972 C LEU 973 O LEU 975 CG LEU 978 N ALA 979 CA ALA 1008 CB ILE
1009 CG1 ILE 1011 CD1 ILE 1209 CD2 LEU 1179 CD1 LEU 977 CD2 LEU
Cavity 17 subcluster 2 residue= 6993 resname=CAV chainid=S
reduced number of grids= 3 corrected number of grids= 14 volume estimate= 0.13 A**3 Formal charge= 0.0
Cavity contact residues: 125 LEU 129 ILE 151 LEU
Cavity contact atoms: 975 CG LEU 977 CD2 LEU 1011 CD1 ILE 1179 CD1 LEU
Cavity 17 subcluster 3 residue= 6994 resname=CAV chainid=S
reduced number of grids= 3 corrected number of grids= 14 volume estimate= 0.13 A**3 Formal charge= 0.0
Cavity contact residues: 129 ILE 151 LEU 155 LEU
Cavity contact atoms: 1011 CD1 ILE 1179 CD1 LEU 1208 CD1 LEU 1209 CD2 LEU 1207 CG LEU
Cavity 17 subcluster 4 residue= 6995 resname=CAV chainid=S
reduced number of grids= 45 corrected number of grids= 74 volume estimate= 0.68 A**3 Formal charge= 0.0
Cavity contact residues: 60 ILE 125 LEU 129 ILE 151 LEU 155 LEU
Cavity contact atoms: 977 CD2 LEU 1011 CD1 ILE 1179 CD1 LEU 477 CD1 ILE 1208 CD1 LEU 975 CG LEU
1178 CG LEU
Cavity 17 subcluster 5 residue= 6996 resname=CAV chainid=S
reduced number of grids= 12 corrected number of grids= 30 volume estimate= 0.28 A**3 Formal charge= 0.0
Cavity contact residues: 60 ILE 125 LEU 151 LEU
Cavity contact atoms: 476 CG2 ILE 477 CD1 ILE 977 CD2 LEU 1178 CG LEU 1179 CD1 LEU
Cavity 25 original number of gridpoints= 189 number of gridpoints left after shaving= 115
Number of subclusters= 76 number of subclusters dropped= 74
Cavity 25 subcluster 1 residue= 6997 resname=CAV chainid=S
reduced number of grids= 114 corrected number of grids= 182 volume estimate= 1.67 A**3 Formal charge= 1.0
Cavity contact residues: 23 LEU 26 TYR 28 LEU 252 ALA 256 ARG
Cavity contact atoms: 208 CD1 TYR 1928 CB ALA 1953 CG ARG 1954 CD ARG 1927 O ALA 189 CD2 LEU
225 CD2 LEU 183 CA LEU 185 O LEU 206 CB TYR 184 C LEU 1925 CA ALA 1926 C ALA 207 CG TYR
176 O GLU
Cavity 25 subcluster 2 residue= 6998 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 7 volume estimate= 0.06 A**3 Formal charge= 0.0
Cavity contact residues: 28 LEU 252 ALA
Cavity contact atoms: 189 CD2 LEU 225 CD2 LEU 1925 CA ALA 1927 O ALA 1953 CG ARG 1926 C ALA
1928 CB ALA
Cavity 31 original number of gridpoints= 48 number of gridpoints left after shaving= 16
Number of subclusters= 33 number of subclusters dropped= 32
Cavity 34 original number of gridpoints= 103 number of gridpoints left after shaving= 64
Number of subclusters= 40 number of subclusters dropped= 39
Cavity 37 original number of gridpoints= 753 number of gridpoints left after shaving= 572
Number of subclusters= 183 number of subclusters dropped= 181
Cavity 37 subcluster 1 residue= 6999 resname=CAV chainid=S
reduced number of grids= 569 corrected number of grids= 739 volume estimate= 6.79 A**3 Formal charge= -1.0
Cavity contact residues: 19 TYR 22 GLU 23 LEU 248 PRO 251 LEU 252 ALA
Cavity contact atoms: 177 CB GLU 182 N LEU 1898 O PRO 1928 CB ALA 187 CG LEU 145 O TYR
188 CD1 LEU 146 CB TYR 1923 CD2 LEU 143 CA TYR 144 C TYR 149 CD2 TYR 189 CD2 LEU 1921 CG LEU
1924 N ALA 1920 CB LEU 1918 C LEU 1925 CA ALA 1896 CA PRO 1897 C PRO 1899 CB PRO 178 CG GLU
40 CD1 LEU 1947 CD1 ILE 147 CG TYR 175 C GLU 1919 O LEU
Cavity 37 subcluster 2 residue= 7000 resname=CAV chainid=S
reduced number of grids= 3 corrected number of grids= 14 volume estimate= 0.13 A**3 Formal charge= 0.0
Cavity contact residues: 5 LEU 19 TYR 23 LEU 251 LEU
Cavity contact atoms: 40 CD1 LEU 146 CB TYR 188 CD1 LEU 1923 CD2 LEU 41 CD2 LEU 144 C TYR
145 O TYR
Cavity 54 original number of gridpoints= 475 number of gridpoints left after shaving= 353
Number of subclusters= 124 number of subclusters dropped= 122
Cavity 54 subcluster 1 residue= 7001 resname=CAV chainid=S
reduced number of grids= 352 corrected number of grids= 470 volume estimate= 4.32 A**3 Formal charge= 1.0
Cavity contact residues: 58 GLY 59 LEU 91 TRP 94 LYS 95 SER 96 VAL 112 LEU
Cavity contact atoms: 728 O TRP 754 C LYS 756 CB LYS 761 N SER 763 C SER 764 O SER
773 CG2 VAL 459 CA GLY 462 N LEU 735 CE3 TRP 460 C GLY 466 CB LEU 467 CG LEU 468 CD1 LEU
729 CB TRP 884 CD2 LEU 883 CD1 LEU 727 C TRP 726 CA TRP
Cavity 54 subcluster 2 residue= 7002 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 0.0
Cavity contact residues:
Cavity contact atoms: 727 C TRP 728 O TRP 729 CB TRP 773 CG2 VAL 884 CD2 LEU
Cavity 55 original number of gridpoints= 21 number of gridpoints left after shaving= 2
Number of subclusters= 21 number of subclusters dropped= 19
Cavity 55 subcluster 1 residue= 7003 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 15 volume estimate= 0.14 A**3 Formal charge= 0.0
Cavity contact residues: 61 PHE 96 VAL 98 VAL 107 VAL
Cavity contact atoms: 484 CD1 PHE 772 CG1 VAL 777 O TYR 792 CG2 VAL 848 CG1 VAL 849 CG2 VAL
Cavity 55 subcluster 2 residue= 7004 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 6 volume estimate= 0.06 A**3 Formal charge= 0.0
Cavity contact residues: 61 PHE 97 TYR
Cavity contact atoms: 772 CG1 VAL 777 O TYR 792 CG2 VAL 484 CD1 PHE 776 C TYR
Cavity 58 original number of gridpoints= 25 number of gridpoints left after shaving= 1
Number of subclusters= 25 number of subclusters dropped= 24
Cavity 65 original number of gridpoints= 23 number of gridpoints left after shaving= 5
Number of subclusters= 19 number of subclusters dropped= 18
Cavity 67 original number of gridpoints= 144 number of gridpoints left after shaving= 77
Number of subclusters= 71 number of subclusters dropped= 67
Cavity 67 subcluster 1 residue= 7005 resname=CAV chainid=S
reduced number of grids= 3 corrected number of grids= 12 volume estimate= 0.11 A**3 Formal charge= 0.0
Cavity contact residues: 60 ILE 151 LEU 155 LEU
Cavity contact atoms: 477 CD1 ILE 1177 CB LEU 1178 CG LEU 1179 CD1 LEU 1208 CD1 LEU 1259 SD MET
1260 CE MET
Cavity 67 subcluster 2 residue= 7006 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 3 volume estimate= 0.03 A**3 Formal charge= 0.0
Cavity contact residues:
Cavity contact atoms: 1177 CB LEU 1178 CG LEU 1259 SD MET 477 CD1 ILE 1179 CD1 LEU
Cavity 67 subcluster 3 residue= 7007 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 3 volume estimate= 0.03 A**3 Formal charge= 0.0
Cavity contact residues:
Cavity contact atoms: 477 CD1 ILE 1177 CB LEU 1178 CG LEU 1259 SD MET
Cavity 67 subcluster 4 residue= 7008 resname=CAV chainid=S
reduced number of grids= 72 corrected number of grids= 126 volume estimate= 1.16 A**3 Formal charge= 0.0
Cavity contact residues: 60 ILE 141 PHE 151 LEU
Cavity contact atoms: 1177 CB LEU 1178 CG LEU 1259 SD MET 477 CD1 ILE 1097 CG PHE 1099 CD2 PHE
1098 CD1 PHE 1101 CE2 PHE 1102 CZ PHE 1100 CE1 PHE 476 CG2 ILE 474 CB ILE
Cavity 69 original number of gridpoints= 24 number of gridpoints left after shaving= 3
Number of subclusters= 22 number of subclusters dropped= 21
Cavity 71 original number of gridpoints= 1400 number of gridpoints left after shaving= 1170
Number of subclusters= 231 number of subclusters dropped= 230
Cavity 85 original number of gridpoints= 297 number of gridpoints left after shaving= 201
Number of subclusters= 98 number of subclusters dropped= 96
Cavity 85 subcluster 1 residue= 7009 resname=CAV chainid=S
reduced number of grids= 200 corrected number of grids= 293 volume estimate= 2.69 A**3 Formal charge= 0.0
Cavity contact residues: 61 PHE 67 VAL 107 VAL 110 ILE 112 LEU
Cavity contact atoms: 844 CA VAL 846 O VAL 848 CG1 VAL 870 CG1 ILE 882 CG LEU 883 CD1 LEU
872 CD1 ILE 486 CE1 PHE 488 CZ PHE 530 CG1 VAL 484 CD1 PHE 849 CG2 VAL 847 CB VAL 845 C VAL
881 CB LEU 531 CG2 VAL
Cavity 85 subcluster 2 residue= 7010 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 4 volume estimate= 0.04 A**3 Formal charge= 0.0
Cavity contact residues: 61 PHE 110 ILE
Cavity contact atoms: 486 CE1 PHE 488 CZ PHE 872 CD1 ILE 883 CD1 LEU 870 CG1 ILE
Cavity 104 original number of gridpoints= 125 number of gridpoints left after shaving= 58
Number of subclusters= 68 number of subclusters dropped= 67
Cavity 105 original number of gridpoints= 52 number of gridpoints left after shaving= 16
Number of subclusters= 39 number of subclusters dropped= 36
Cavity 105 subcluster 1 residue= 7011 resname=CAV chainid=S
reduced number of grids= 13 corrected number of grids= 36 volume estimate= 0.33 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 23 LEU 28 LEU 255 ILE
Cavity contact atoms: 24 CG1 VAL 25 CG2 VAL 189 CD2 LEU 223 CG LEU 225 CD2 LEU 1946 CG2 ILE
222 CB LEU 23 CB VAL
Cavity 105 subcluster 2 residue= 7012 resname=CAV chainid=S
reduced number of grids= 2 corrected number of grids= 11 volume estimate= 0.10 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 23 LEU 255 ILE
Cavity contact atoms: 23 CB VAL 24 CG1 VAL 25 CG2 VAL 189 CD2 LEU 1946 CG2 ILE 1947 CD1 ILE
188 CD1 LEU
Cavity 105 subcluster 3 residue= 7013 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 23 LEU 28 LEU
Cavity contact atoms: 25 CG2 VAL 189 CD2 LEU 222 CB LEU 223 CG LEU 225 CD2 LEU 24 CG1 VAL
186 CB LEU 187 CG LEU
Cavity 109 original number of gridpoints= 38 number of gridpoints left after shaving= 13
Number of subclusters= 27 number of subclusters dropped= 25
Cavity 109 subcluster 1 residue= 7014 resname=CAV chainid=S
reduced number of grids= 3 corrected number of grids= 13 volume estimate= 0.12 A**3 Formal charge= 0.0
Cavity contact residues: 60 ILE 139 LEU 140 LEU
Cavity contact atoms: 475 CG1 ILE 477 CD1 ILE 1078 C LEU 1080 CB LEU 1084 N LEU 1086 C LEU
1087 O LEU 1096 CB PHE 1079 O LEU 1092 N PHE
Cavity 109 subcluster 2 residue= 7015 resname=CAV chainid=S
reduced number of grids= 10 corrected number of grids= 25 volume estimate= 0.23 A**3 Formal charge= 0.0
Cavity contact residues: 60 ILE 139 LEU 140 LEU 141 PHE
Cavity contact atoms: 477 CD1 ILE 1078 C LEU 1079 O LEU 1080 CB LEU 1086 C LEU 1087 O LEU
1092 N PHE 1096 CB PHE 1084 N LEU 1258 CG MET 1259 SD MET 475 CG1 ILE 1093 CA PHE 474 CB ILE
Cavity 125 original number of gridpoints= 37 number of gridpoints left after shaving= 15
Number of subclusters= 23 number of subclusters dropped= 22
Cavity 128 original number of gridpoints= 277 number of gridpoints left after shaving= 185
Number of subclusters= 93 number of subclusters dropped= 92
Cavity 132 original number of gridpoints= 501 number of gridpoints left after shaving= 391
Number of subclusters= 113 number of subclusters dropped= 110
Cavity 132 subcluster 1 residue= 7016 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 0.0
Cavity contact residues: 5 LEU 23 LEU 255 ILE
Cavity contact atoms: 25 CG2 VAL 41 CD2 LEU 188 CD1 LEU 1947 CD1 ILE
Cavity 132 subcluster 2 residue= 7017 resname=CAV chainid=S
reduced number of grids= 389 corrected number of grids= 493 volume estimate= 4.53 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 4 LEU 5 LEU 192 SER 194 THR 255 ILE
Cavity contact atoms: 23 CB VAL 25 CG2 VAL 41 CD2 LEU 1947 CD1 ILE 29 O LEU 26 N LEU
28 C LEU 1489 O SER 1488 C SER 1491 OG SER 1492 N ILE 1493 CA ILE 1500 N THR 1505 OG1 THR
1494 C ILE 1490 CB SER 21 C VAL 188 CD1 LEU 24 CG1 VAL 1946 CG2 ILE 34 N LEU 1945 CG1 ILE
Cavity 132 subcluster 3 residue= 7018 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 3 volume estimate= 0.03 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 255 ILE
Cavity contact atoms: 24 CG1 VAL 1491 OG SER 1946 CG2 ILE 1947 CD1 ILE 23 CB VAL 1490 CB SER
Cavity 147 original number of gridpoints= 30 number of gridpoints left after shaving= 10
Number of subclusters= 22 number of subclusters dropped= 20
Cavity 147 subcluster 1 residue= 7019 resname=CAV chainid=S
reduced number of grids= 9 corrected number of grids= 25 volume estimate= 0.23 A**3 Formal charge= 0.0
Cavity contact residues: 1 MET 3 VAL 28 LEU 259 LEU
Cavity contact atoms: 3 C MET 4 O MET 5 CB MET 223 CG LEU 224 CD1 LEU 1979 CD1 LEU
24 CG1 VAL
Cavity 147 subcluster 2 residue= 7020 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 259 LEU
Cavity contact atoms: 4 O MET 5 CB MET 24 CG1 VAL 1979 CD1 LEU 3 C MET
Cavity 160 original number of gridpoints= 197 number of gridpoints left after shaving= 95
Number of subclusters= 110 number of subclusters dropped= 102
Cavity 160 subcluster 1 residue= 7021 resname=CAV chainid=S
reduced number of grids= 85 corrected number of grids= 152 volume estimate= 1.40 A**3 Formal charge= 0.0
Cavity contact residues: 5 LEU 20 ILE 30 ALA 31 THR 32 LEU
Cavity contact atoms: 40 CD1 LEU 158 CB ILE 160 CG2 ILE 239 CB ALA 39 CG LEU 240 N THR
242 C THR 237 C ALA 241 CA THR 243 O THR 247 N LEU 38 CB LEU 251 CB LEU 248 CA LEU
238 O ALA 155 CA ILE
Cavity 160 subcluster 2 residue= 7022 resname=CAV chainid=S
reduced number of grids= 4 corrected number of grids= 15 volume estimate= 0.14 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 5 LEU 30 ALA 31 THR
Cavity contact atoms: 22 O VAL 34 N LEU 39 CG LEU 239 CB ALA 240 N THR 243 O THR
21 C VAL 242 C THR 28 C LEU 236 CA ALA 237 C ALA 25 CG2 VAL
Cavity 160 subcluster 3 residue= 7023 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 6 volume estimate= 0.06 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 5 LEU
Cavity contact atoms: 21 C VAL 22 O VAL 28 C LEU 34 N LEU 39 CG LEU 239 CB ALA
240 N THR 243 O THR 27 CA LEU 26 N LEU
Cavity 160 subcluster 4 residue= 7024 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 3 volume estimate= 0.03 A**3 Formal charge= 0.0
Cavity contact residues: 5 LEU
Cavity contact atoms: 22 O VAL 25 CG2 VAL 28 C LEU 34 N LEU 39 CG LEU 239 CB ALA
21 C VAL 27 CA LEU 243 O THR 41 CD2 LEU
Cavity 160 subcluster 5 residue= 7025 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 4 volume estimate= 0.04 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 5 LEU
Cavity contact atoms: 21 C VAL 22 O VAL 25 CG2 VAL 26 N LEU 27 CA LEU 28 C LEU
34 N LEU 39 CG LEU 41 CD2 LEU 243 O THR
Cavity 160 subcluster 6 residue= 7026 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 4 volume estimate= 0.04 A**3 Formal charge= 0.0
Cavity contact residues: 30 ALA
Cavity contact atoms: 22 O VAL 25 CG2 VAL 39 CG LEU 239 CB ALA 21 C VAL 34 N LEU
Cavity 160 subcluster 7 residue= 7027 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 6 volume estimate= 0.06 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL
Cavity contact atoms: 21 C VAL 22 O VAL 25 CG2 VAL 34 N LEU 39 CG LEU 41 CD2 LEU
239 CB ALA 26 N LEU 28 C LEU
Cavity 160 subcluster 8 residue= 7028 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 7 volume estimate= 0.06 A**3 Formal charge= 0.0
Cavity contact residues: 3 VAL 4 LEU 5 LEU
Cavity contact atoms: 22 O VAL 25 CG2 VAL 26 N LEU 27 CA LEU 28 C LEU 34 N LEU
39 CG LEU 41 CD2 LEU 21 C VAL
Cavity 161 original number of gridpoints= 24 number of gridpoints left after shaving= 7
Number of subclusters= 20 number of subclusters dropped= 17
Cavity 161 subcluster 1 residue= 7029 resname=CAV chainid=S
reduced number of grids= 5 corrected number of grids= 15 volume estimate= 0.14 A**3 Formal charge= 0.0
Cavity contact residues: 50 LEU 59 LEU 83 TRP 91 TRP
Cavity contact atoms: 399 CD1 LEU 468 CD1 LEU 660 CZ3 TRP 661 CH2 TRP 730 CG TRP 731 CD1 TRP
732 CD2 TRP 734 CE2 TRP 400 CD2 LEU 733 NE1 TRP
Cavity 161 subcluster 2 residue= 7030 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 4 volume estimate= 0.04 A**3 Formal charge= 0.0
Cavity contact residues: 50 LEU 59 LEU 91 TRP
Cavity contact atoms: 400 CD2 LEU 468 CD1 LEU 730 CG TRP 731 CD1 TRP 732 CD2 TRP 733 NE1 TRP
734 CE2 TRP 399 CD1 LEU
Cavity 161 subcluster 3 residue= 7031 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 0.0
Cavity contact residues: 50 LEU 91 TRP
Cavity contact atoms: 399 CD1 LEU 400 CD2 LEU 660 CZ3 TRP 661 CH2 TRP 730 CG TRP 731 CD1 TRP
732 CD2 TRP 733 NE1 TRP 734 CE2 TRP 468 CD1 LEU
Cavity 163 original number of gridpoints= 21 number of gridpoints left after shaving= 6
Number of subclusters= 18 number of subclusters dropped= 15
Cavity 163 subcluster 1 residue= 7032 resname=CAV chainid=S
reduced number of grids= 4 corrected number of grids= 12 volume estimate= 0.11 A**3 Formal charge= 0.0
Cavity contact residues: 1 MET 3 VAL 191 ALA 259 LEU
Cavity contact atoms: 5 CB MET 24 CG1 VAL 1485 CB ALA 1979 CD1 LEU 12 O LYS 3 C MET
Cavity 163 subcluster 2 residue= 7033 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 4 volume estimate= 0.04 A**3 Formal charge= 1.0
Cavity contact residues: 2 LYS
Cavity contact atoms: 3 C MET 5 CB MET 9 N LYS 11 C LYS 12 O LYS 24 CG1 VAL
1485 CB ALA 4 O MET
Cavity 163 subcluster 3 residue= 7034 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 1.0
Cavity contact residues: 2 LYS 3 VAL
Cavity contact atoms: 5 CB MET 12 O LYS 24 CG1 VAL 1485 CB ALA 3 C MET 11 C LYS
1979 CD1 LEU 9 N LYS
Cavity 172 original number of gridpoints= 371 number of gridpoints left after shaving= 266
Number of subclusters= 106 number of subclusters dropped= 105
Cavity 176 original number of gridpoints= 33 number of gridpoints left after shaving= 9
Number of subclusters= 26 number of subclusters dropped= 24
Cavity 176 subcluster 1 residue= 7035 resname=CAV chainid=S
reduced number of grids= 8 corrected number of grids= 30 volume estimate= 0.28 A**3 Formal charge= 0.0
Cavity contact residues: 193 ILE 195 PHE 221 PHE 222 ALA 232 LEU
Cavity contact atoms: 1495 O ILE 1513 CD1 PHE 1718 CB PHE 1725 N ALA 1728 O ALA 1795 CD1 LEU
1721 CD2 PHE 1715 CA PHE 1515 CE1 PHE 1719 CG PHE 1716 C PHE 1796 CD2 LEU
Cavity 176 subcluster 2 residue= 7036 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 3 volume estimate= 0.03 A**3 Formal charge= 0.0
Cavity contact residues:
Cavity contact atoms: 1513 CD1 PHE 1718 CB PHE 1725 N ALA 1728 O ALA 1495 O ILE 1795 CD1 LEU
Cavity 181 original number of gridpoints= 54 number of gridpoints left after shaving= 22
Number of subclusters= 34 number of subclusters dropped= 32
Cavity 181 subcluster 1 residue= 7037 resname=CAV chainid=S
reduced number of grids= 21 corrected number of grids= 48 volume estimate= 0.44 A**3 Formal charge= -1.0
Cavity contact residues: 141 PHE 143 CYS 146 LEU 149 GLU 152 PRO 164 SER
Cavity contact atoms: 1101 CE2 PHE 1160 CB GLU 1161 CG GLU 1186 CG PRO 1135 CD2 LEU 1099 CD2 PHE
1115 SG CYS 1275 OG SER 1274 CB SER
Cavity 181 subcluster 2 residue= 7038 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 6 volume estimate= 0.06 A**3 Formal charge= 0.0
Cavity contact residues: 164 SER
Cavity contact atoms: 1099 CD2 PHE 1101 CE2 PHE 1115 SG CYS 1186 CG PRO 1274 CB SER 1275 OG SER
1135 CD2 LEU
Cavity 193 original number of gridpoints= 143 number of gridpoints left after shaving= 81
Number of subclusters= 65 number of subclusters dropped= 62
Cavity 193 subcluster 1 residue= 7039 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 0.0
Cavity contact residues: 197 SER
Cavity contact atoms: 67 OD1 ASP 283 CD1 LEU 1534 OG SER 1546 CB SER
Cavity 193 subcluster 2 residue= 7040 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 8 volume estimate= 0.07 A**3 Formal charge= 0.0
Cavity contact residues: 36 LEU 197 SER 199 SER
Cavity contact atoms: 282 CG LEU 283 CD1 LEU 1534 OG SER 1546 CB SER 284 CD2 LEU 67 OD1 ASP
Cavity 193 subcluster 3 residue= 7041 resname=CAV chainid=S
reduced number of grids= 79 corrected number of grids= 130 volume estimate= 1.19 A**3 Formal charge= -1.0
Cavity contact residues: 8 ASP 35 VAL 36 LEU 197 SER 199 SER 200 GLY 203 TYR
Cavity contact atoms: 67 OD1 ASP 282 CG LEU 283 CD1 LEU 1534 OG SER 1546 CB SER 284 CD2 LEU
1548 N GLY 1544 C SER 1549 CA GLY 276 CG2 VAL 1573 CD1 TYR 1575 CE1 TYR 1545 O SER
Cavity 201 original number of gridpoints= 547 number of gridpoints left after shaving= 354
Number of subclusters= 197 number of subclusters dropped= 193
Cavity 201 subcluster 1 residue= 7042 resname=CAV chainid=S
reduced number of grids= 351 corrected number of grids= 533 volume estimate= 4.90 A**3 Formal charge= 0.0
Cavity contact residues: 195 PHE 201 LEU 205 LEU 208 ILE 216 ILE 221 PHE 232 LEU 237 LEU
Cavity contact atoms: 1719 CG PHE 1721 CD2 PHE 1723 CE2 PHE 1796 CD2 LEU 1825 CG LEU 1591 CD1 LEU
1515 CE1 PHE 1724 CZ PHE 1826 CD1 LEU 1517 CZ PHE 1558 CD1 LEU 1827 CD2 LEU 1619 CD1 ILE 1618 CG2 ILE
1616 CB ILE 1679 CD1 ILE 1720 CD1 PHE 1824 CB LEU 1722 CE1 PHE
Cavity 201 subcluster 2 residue= 7043 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 6 volume estimate= 0.06 A**3 Formal charge= 0.0
Cavity contact residues: 205 LEU 221 PHE 237 LEU
Cavity contact atoms: 1591 CD1 LEU 1724 CZ PHE 1825 CG LEU 1826 CD1 LEU 1723 CE2 PHE
Cavity 201 subcluster 3 residue= 7044 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 0.0
Cavity contact residues: 205 LEU 216 ILE
Cavity contact atoms: 1679 CD1 ILE 1826 CD1 LEU 1591 CD1 LEU 1724 CZ PHE
Cavity 201 subcluster 4 residue= 7045 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 3 volume estimate= 0.03 A**3 Formal charge= 0.0
Cavity contact residues: 205 LEU 221 PHE
Cavity contact atoms: 1591 CD1 LEU 1724 CZ PHE 1723 CE2 PHE 1618 CG2 ILE
Cavity 209 original number of gridpoints= 58 number of gridpoints left after shaving= 22
Number of subclusters= 39 number of subclusters dropped= 36
Cavity 209 subcluster 1 residue= 7046 resname=CAV chainid=S
reduced number of grids= 18 corrected number of grids= 42 volume estimate= 0.39 A**3 Formal charge= 1.0
Cavity contact residues: 46 PHE 49 LYS 140 LEU 165 ILE
Cavity contact atoms: 363 CD1 PHE 1090 CD1 LEU 1091 CD2 LEU 1282 CG2 ILE 389 CD LYS 387 CB LYS
365 CE1 PHE 1089 CG LEU 388 CG LYS
Cavity 209 subcluster 2 residue= 7047 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 1.0
Cavity contact residues: 46 PHE 49 LYS 165 ILE
Cavity contact atoms: 389 CD LYS 1282 CG2 ILE 1283 CD1 ILE 363 CD1 PHE 358 CA PHE
Cavity 209 subcluster 3 residue= 7048 resname=CAV chainid=S
reduced number of grids= 3 corrected number of grids= 11 volume estimate= 0.10 A**3 Formal charge= 1.0
Cavity contact residues: 46 PHE 49 LYS 165 ILE
Cavity contact atoms: 358 CA PHE 363 CD1 PHE 389 CD LYS 1283 CD1 ILE 1282 CG2 ILE 387 CB LYS
388 CG LYS
Cavity 211 original number of gridpoints= 33 number of gridpoints left after shaving= 12
Number of subclusters= 22 number of subclusters dropped= 21
Cavity 223 original number of gridpoints= 87 number of gridpoints left after shaving= 30
Number of subclusters= 61 number of subclusters dropped= 57
Cavity 223 subcluster 1 residue= 7049 resname=CAV chainid=S
reduced number of grids= 26 corrected number of grids= 64 volume estimate= 0.59 A**3 Formal charge= 1.0
Cavity contact residues: 38 PHE 40 PHE 65 ARG 168 TYR
Cavity contact atoms: 295 CB PHE 296 CG PHE 297 CD1 PHE 514 CG ARG 515 CD ARG 1302 CB TYR
1304 CD1 TYR 513 CB ARG 1303 CG TYR 320 CE2 PHE 305 O GLU 318 CD2 PHE 299 CE1 PHE
Cavity 223 subcluster 2 residue= 7050 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 4 volume estimate= 0.04 A**3 Formal charge= -1.0
Cavity contact residues: 38 PHE 39 GLU
Cavity contact atoms: 297 CD1 PHE 304 C GLU 305 O GLU 318 CD2 PHE 320 CE2 PHE 1302 CB TYR
Cavity 223 subcluster 3 residue= 7051 resname=CAV chainid=S
reduced number of grids= 2 corrected number of grids= 14 volume estimate= 0.13 A**3 Formal charge= -1.0
Cavity contact residues: 38 PHE 39 GLU 168 TYR
Cavity contact atoms: 304 C GLU 305 O GLU 318 CD2 PHE 320 CE2 PHE 1302 CB TYR 297 CD1 PHE
Cavity 223 subcluster 4 residue= 7052 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 1.0
Cavity contact residues: 40 PHE 65 ARG
Cavity contact atoms: 297 CD1 PHE 320 CE2 PHE 321 CZ PHE 513 CB ARG 515 CD ARG 1302 CB TYR
299 CE1 PHE 514 CG ARG
Cavity 239 original number of gridpoints= 36 number of gridpoints left after shaving= 14
Number of subclusters= 23 number of subclusters dropped= 22
Cavity 249 original number of gridpoints= 134 number of gridpoints left after shaving= 73
Number of subclusters= 62 number of subclusters dropped= 61
Cavity 264 original number of gridpoints= 22 number of gridpoints left after shaving= 5
Number of subclusters= 18 number of subclusters dropped= 17
Cavity 277 original number of gridpoints= 102 number of gridpoints left after shaving= 36
Number of subclusters= 71 number of subclusters dropped= 66
Cavity 277 subcluster 1 residue= 7053 resname=CAV chainid=S
reduced number of grids= 27 corrected number of grids= 59 volume estimate= 0.54 A**3 Formal charge= 0.0
Cavity contact residues: 6 LEU 33 ILE 34 PRO 35 VAL 176 ILE
Cavity contact atoms: 51 CD2 LEU 261 CG2 ILE 266 O PRO 275 CG1 VAL 1364 CG1 ILE 1365 CG2 ILE
1363 CB ILE 265 C PRO
Cavity 277 subcluster 2 residue= 7054 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 6 volume estimate= 0.06 A**3 Formal charge= 0.0
Cavity contact residues: 6 LEU 33 ILE 176 ILE
Cavity contact atoms: 261 CG2 ILE 1365 CG2 ILE 51 CD2 LEU
Cavity 277 subcluster 3 residue= 7055 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 4 volume estimate= 0.04 A**3 Formal charge= 0.0
Cavity contact residues: 6 LEU 176 ILE
Cavity contact atoms: 51 CD2 LEU 275 CG1 VAL 1364 CG1 ILE 1365 CG2 ILE
Cavity 277 subcluster 4 residue= 7056 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 10 volume estimate= 0.09 A**3 Formal charge= 0.0
Cavity contact residues: 35 VAL 176 ILE
Cavity contact atoms: 275 CG1 VAL 1364 CG1 ILE 1365 CG2 ILE 1583 CB SER 51 CD2 LEU 1366 CD1 ILE
Cavity 277 subcluster 5 residue= 7057 resname=CAV chainid=S
reduced number of grids= 6 corrected number of grids= 23 volume estimate= 0.21 A**3 Formal charge= 0.0
Cavity contact residues: 6 LEU 33 ILE 176 ILE 180 LEU
Cavity contact atoms: 51 CD2 LEU 261 CG2 ILE 1365 CG2 ILE 1393 CG LEU 1394 CD1 LEU 1362 O ILE
Cavity 293 original number of gridpoints= 76 number of gridpoints left after shaving= 45
Number of subclusters= 32 number of subclusters dropped= 31
Cavity 299 original number of gridpoints= 25 number of gridpoints left after shaving= 6
Number of subclusters= 22 number of subclusters dropped= 19
Cavity 299 subcluster 1 residue= 7058 resname=CAV chainid=S
reduced number of grids= 1 corrected number of grids= 7 volume estimate= 0.06 A**3 Formal charge= 0.0
Cavity contact residues: 189 VAL 212 SER 215 ASN
Cavity contact atoms: 1472 CG1 VAL 1650 CB SER 1666 C ASN 1667 O ASN 1668 CB ASN 1672 N ILE
1704 CD1 ILE 1647 CA SER
Cavity 299 subcluster 2 residue= 7059 resname=CAV chainid=S
reduced number of grids= 2 corrected number of grids= 7 volume estimate= 0.06 A**3 Formal charge= 0.0
Cavity contact residues: 189 VAL 212 SER
Cavity contact atoms: 1647 CA SER 1649 O SER 1650 CB SER 1666 C ASN 1667 O ASN 1668 CB ASN
1472 CG1 VAL 1672 N ILE 1473 CG2 VAL
Cavity 299 subcluster 3 residue= 7060 resname=CAV chainid=S
reduced number of grids= 3 corrected number of grids= 11 volume estimate= 0.10 A**3 Formal charge= 0.0
Cavity contact residues: 189 VAL 212 SER 215 ASN
Cavity contact atoms: 1472 CG1 VAL 1473 CG2 VAL 1647 CA SER 1648 C SER 1649 O SER 1650 CB SER
1666 C ASN 1668 CB ASN 1651 OG SER
Cavity 300 original number of gridpoints= 145 number of gridpoints left after shaving= 80
Number of subclusters= 66 number of subclusters dropped= 65
Cavity 314 original number of gridpoints= 123 number of gridpoints left after shaving= 75
Number of subclusters= 50 number of subclusters dropped= 48
Cavity 314 subcluster 1 residue= 7061 resname=CAV chainid=S
reduced number of grids= 73 corrected number of grids= 115 volume estimate= 1.06 A**3 Formal charge= 0.0
Cavity contact residues: 180 LEU 184 TYR 208 ILE 211 LEU
Cavity contact atoms: 1395 CD2 LEU 1430 CE1 TYR 1644 CD1 LEU 1392 CB LEU 1613 CA ILE 1394 CD1 LEU
1605 O HIS 1393 CG LEU 1612 N ILE 1604 C HIS 1617 CG1 ILE 1642 CB LEU 1432 CZ TYR 1433 OH TYR
1615 O ILE 1614 C ILE
Cavity 314 subcluster 2 residue= 7062 resname=CAV chainid=S
reduced number of grids= 2 corrected number of grids= 8 volume estimate= 0.07 A**3 Formal charge= 0.0
Cavity contact residues: 180 LEU 207 HIS 208 ILE 211 LEU
Cavity contact atoms: 1394 CD1 LEU 1604 C HIS 1605 O HIS 1612 N ILE 1613 CA ILE 1644 CD1 LEU
1392 CB LEU 1617 CG1 ILE
+++++ Closing unit 10
Circular variance filtering of 11076324 gridpoints (grid cluster # 1)
Pocket gridpoints form 99 clusters
Number of pocket clusters containing more than 108 gridpoints= 10
File f8_3.pdb is already present
File f8_4.pdb is already present
File f8_5.pdb is already present
File f8_6.pdb is already present
File f8_7.pdb is already present
File f8_8.pdb is already present
+++++ FORMATTED file f8_9.pdb as unit 10, Mode=NEW, type=15 has been opened
Pocket 5 residue 261 resname=PCK chainid=G # of grids= 1575 volume estimate= 14.47 A**3 Formal charge= -1.0
Pocket contact residues: 46 PHE 50 LEU 59 LEU 61 PHE 67 VAL 70 ALA 71 GLU 74 LEU 83 TRP
Pocket contact residues: 110 ILE 112 LEU 142 PRO
Pocket contact atoms: 552 CA GLU 580 CD1 LEU 551 N GLU 548 C ALA 549 O ALA 550 CB ALA
398 CD1 LEU 579 CG LEU 660 CZ3 TRP 661 CH2 TRP 658 CE3 TRP 659 CZ2 TRP 556 CG GLU 872 CD1 ILE
399 CD1 LEU 657 CE2 TRP 871 CG2 ILE 555 CB GLU 656 NE1 TRP 654 CD1 TRP 869 CB ILE 528 O VAL
488 CZ PHE 400 CD2 LEU 367 CZ PHE 365 CE1 PHE 469 CD2 LEU 468 CD1 LEU 487 CE2 PHE 1108 CG PRO
486 CE1 PHE 883 CD1 LEU
Pocket 7 residue 262 resname=PCK chainid=G # of grids= 3275 volume estimate= 30.08 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 13 residue 263 resname=PCK chainid=G # of grids= 688 volume estimate= 6.32 A**3 Formal charge= -1.0
Pocket contact residues: 96 VAL 98 VAL 104 ALA 107 VAL 112 LEU 113 ASP 114 THR
Pocket contact atoms: 825 CA ALA 827 O ALA 847 CB VAL 826 C ALA 848 CG1 VAL 792 CG2 VAL
893 N THR 772 CG1 VAL 880 O LEU 888 O ASP 771 CB VAL 881 CB LEU 894 CA THR 828 CB ALA
770 O VAL 769 C VAL 887 C ASP 850 N SER 790 CB VAL 791 CG1 VAL 911 C GLY 910 CA GLY
Pocket 14 residue 264 resname=PCK chainid=G # of grids= 4336 volume estimate= 39.82 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 40 residue 265 resname=PCK chainid=G # of grids= 1484 volume estimate= 13.63 A**3 Formal charge= 0.0
Pocket contact residues: 97 TYR 129 ILE 134 SER 135 SER 137 LEU 139 LEU 160 ILE 161 ALA
Pocket contact atoms: 1064 O LEU 1076 N LEU 1081 CG LEU 1251 O ALA 1246 CG2 ILE 1248 N ALA
1083 CD2 LEU 1048 CB SER 1082 CD1 LEU 1053 O SER 1050 N SER 1045 CA SER 1010 CG2 ILE 1247 CD1 ILE
1245 CG1 ILE 785 OH TYR 782 CE1 TYR 784 CZ TYR 1009 CG1 ILE 1011 CD1 ILE 1007 O ILE 1038 O GLU
Pocket 42 residue 266 resname=PCK chainid=G # of grids= 623 volume estimate= 5.72 A**3 Formal charge= 0.0
Pocket contact residues: 6 LEU 35 VAL 195 PHE 196 PHE 197 SER 200 GLY 201 LEU 204 SER
Pocket contact atoms: 276 CG2 VAL 1534 OG SER 1549 CA GLY 45 O LEU 1550 C GLY 1514 CD2 PHE
1552 N LEU 1551 O GLY 275 CG1 VAL 46 CB LEU 1584 OG SER 50 CD2 LEU 1532 O SER 1511 CB PHE
1512 CG PHE 44 C LEU 1518 N PHE 1529 N SER 1508 CA PHE 1548 N GLY 53 CA LYS 54 C LYS
1509 C PHE 61 N ASP 52 N LYS 1519 CA PHE 1522 CB PHE
Pocket 51 residue 267 resname=PCK chainid=G # of grids= 876 volume estimate= 8.05 A**3 Formal charge= -1.0
Pocket contact residues: 62 THR 63 SER 66 ALA 141 PHE 142 PRO 143 CYS 144 GLY 149 GLU 168 TYR
Pocket contact atoms: 1164 OE2 GLU 1309 OH TYR 1116 N GLY 1307 CE2 TYR 1111 CA CYS 1308 CZ TYR
1112 C CYS 1114 CB CYS 494 OG1 THR 1102 CZ PHE 1100 CE1 PHE 1106 O PRO 524 CB ALA 1162 CD GLU
500 CB SER 496 N SER 489 N THR 491 C THR 479 CA PHE 497 CA SER 499 O SER 480 C PHE
490 CA THR 1098 CD1 PHE
Pocket 52 residue 268 resname=PCK chainid=G # of grids= 377 volume estimate= 3.46 A**3 Formal charge= -1.0
Pocket contact residues: 62 THR 122 ALA 141 PHE 149 GLU 150 ILE 151 LEU 152 PRO
Pocket contact atoms: 1163 OE1 GLU 1165 N ILE 1173 N LEU 1157 CA GLU 1180 CD2 LEU 1177 CB LEU
1160 CB GLU 1101 CE2 PHE 1187 CD PRO 1102 CZ PHE 1170 CG1 ILE 1158 C GLU 494 OG1 THR 495 CG2 THR
493 CB THR 951 CB ALA 948 CA ALA
Pocket 89 residue 269 resname=PCK chainid=G # of grids= 118 volume estimate= 1.08 A**3 Formal charge= 0.0
Pocket contact residues: 97 TYR 98 VAL 118 THR 125 LEU
Pocket contact atoms: 775 CA TYR 778 CB TYR 779 CG TYR 781 CD2 TYR 976 CD1 LEU 786 N VAL
776 C TYR 789 O VAL 925 O THR 788 C VAL 975 CG LEU 977 CD2 LEU 799 CG2 VAL 787 CA VAL
933 CB CYS 974 CB LEU 934 SG CYS 929 N CYS
Pocket 95 residue 270 resname=PCK chainid=G # of grids= 331 volume estimate= 3.04 A**3 Formal charge= 1.0
Pocket contact residues: 47 SER 50 LEU 51 SER 74 LEU 79 LYS 83 TRP 87 LEU
Pocket contact atoms: 371 O SER 406 CB SER 620 CB LYS 621 CG LYS 622 CD LYS 581 CD2 LEU
402 N SER 694 CD1 LEU 369 CA SER 370 C SER 372 CB SER 403 CA SER 396 CB LEU 394 C LEU
395 O LEU 658 CE3 TRP 660 CZ3 TRP 398 CD1 LEU
A total of 13683 pocket gridpoints were written to file f8_9.pdb
Residue number of the first pocket= 261
Attempting to find subclusters by shaving 1 layers off each cluster
Grids with 3, or less neighbors will be considered surface grids and will be shaved off
Grids shaved off as surface grids will be put back to the subcluster they were shaved off from
Pocket 5 original number of gridpoints= 1575 number of gridpoints left after shaving= 1169
Number of subclusters= 409 number of subclusters dropped= 406
Pocket 5 subcluster 1 residue= 271 resname=PCK chainid=S
reduced number of grids= 1166 corrected number of grids= 1561 volume estimate= 14.34 A**3 Formal charge= -1.0
Pocket contact residues: 46 PHE 50 LEU 59 LEU 61 PHE 70 ALA 71 GLU 74 LEU 83 TRP 110 ILE
Pocket contact residues: 112 LEU 142 PRO
Pocket contact atoms: 552 CA GLU 580 CD1 LEU 551 N GLU 548 C ALA 549 O ALA 550 CB ALA
872 CD1 ILE 398 CD1 LEU 661 CH2 TRP 660 CZ3 TRP 659 CZ2 TRP 399 CD1 LEU 657 CE2 TRP 556 CG GLU
871 CG2 ILE 555 CB GLU 488 CZ PHE 400 CD2 LEU 468 CD1 LEU 469 CD2 LEU 367 CZ PHE 365 CE1 PHE
656 NE1 TRP 654 CD1 TRP 869 CB ILE 883 CD1 LEU 486 CE1 PHE 579 CG LEU 658 CE3 TRP 528 O VAL
487 CE2 PHE 1108 CG PRO
Pocket 5 subcluster 2 residue= 272 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 3 volume estimate= 0.03 A**3 Formal charge= 0.0
Pocket contact residues: 46 PHE 50 LEU 59 LEU
Pocket contact atoms: 365 CE1 PHE 367 CZ PHE 399 CD1 LEU 400 CD2 LEU 469 CD2 LEU
Pocket 5 subcluster 3 residue= 273 resname=PCK chainid=S
reduced number of grids= 2 corrected number of grids= 11 volume estimate= 0.10 A**3 Formal charge= -1.0
Pocket contact residues: 67 VAL 71 GLU 110 ILE
Pocket contact atoms: 528 O VAL 551 N GLU 871 CG2 ILE 872 CD1 ILE 555 CB GLU 552 CA GLU
550 CB ALA
Pocket 7 original number of gridpoints= 3275 number of gridpoints left after shaving= 2703
Number of subclusters= 575 number of subclusters dropped= 572
Pocket 7 subcluster 1 residue= 274 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 6 volume estimate= 0.06 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 7 subcluster 2 residue= 275 resname=PCK chainid=S
reduced number of grids= 2701 corrected number of grids= 3265 volume estimate= 29.99 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 7 subcluster 3 residue= 276 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 4 volume estimate= 0.04 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 13 original number of gridpoints= 688 number of gridpoints left after shaving= 518
Number of subclusters= 171 number of subclusters dropped= 170
Pocket 14 original number of gridpoints= 4336 number of gridpoints left after shaving= 3404
Number of subclusters= 943 number of subclusters dropped= 932
Pocket 14 subcluster 1 residue= 277 resname=PCK chainid=S
reduced number of grids= 3388 corrected number of grids= 4275 volume estimate= 39.26 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 14 subcluster 2 residue= 278 resname=PCK chainid=S
reduced number of grids= 6 corrected number of grids= 20 volume estimate= 0.18 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 14 subcluster 3 residue= 279 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 3 volume estimate= 0.03 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 14 subcluster 4 residue= 280 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 14 subcluster 5 residue= 281 resname=PCK chainid=S
reduced number of grids= 2 corrected number of grids= 7 volume estimate= 0.06 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 14 subcluster 6 residue= 282 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 3 volume estimate= 0.03 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 14 subcluster 7 residue= 283 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 2 volume estimate= 0.02 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 14 subcluster 8 residue= 284 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 4 volume estimate= 0.04 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 14 subcluster 9 residue= 285 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 14 subcluster 10 residue= 286 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 4 volume estimate= 0.04 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 14 subcluster 11 residue= 287 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 8 volume estimate= 0.07 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms:
Pocket 40 original number of gridpoints= 1484 number of gridpoints left after shaving= 1185
Number of subclusters= 302 number of subclusters dropped= 299
Pocket 40 subcluster 1 residue= 288 resname=PCK chainid=S
reduced number of grids= 1183 corrected number of grids= 1474 volume estimate= 13.54 A**3 Formal charge= 0.0
Pocket contact residues: 97 TYR 129 ILE 134 SER 135 SER 137 LEU 139 LEU 160 ILE 161 ALA
Pocket contact atoms: 1064 O LEU 1076 N LEU 1081 CG LEU 1251 O ALA 1246 CG2 ILE 1248 N ALA
1048 CB SER 1082 CD1 LEU 1050 N SER 1083 CD2 LEU 1010 CG2 ILE 1045 CA SER 1247 CD1 ILE 785 OH TYR
782 CE1 TYR 784 CZ TYR 1009 CG1 ILE 1011 CD1 ILE 1007 O ILE 1053 O SER 1245 CG1 ILE 1038 O GLU
Pocket 40 subcluster 2 residue= 289 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 4 volume estimate= 0.04 A**3 Formal charge= 0.0
Pocket contact residues: 139 LEU
Pocket contact atoms: 1081 CG LEU 1083 CD2 LEU
Pocket 40 subcluster 3 residue= 290 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 6 volume estimate= 0.06 A**3 Formal charge= 0.0
Pocket contact residues: 129 ILE
Pocket contact atoms: 1010 CG2 ILE 1007 O ILE
Pocket 42 original number of gridpoints= 623 number of gridpoints left after shaving= 476
Number of subclusters= 148 number of subclusters dropped= 147
Pocket 51 original number of gridpoints= 876 number of gridpoints left after shaving= 693
Number of subclusters= 184 number of subclusters dropped= 183
Pocket 52 original number of gridpoints= 377 number of gridpoints left after shaving= 233
Number of subclusters= 150 number of subclusters dropped= 144
Pocket 52 subcluster 1 residue= 291 resname=PCK chainid=S
reduced number of grids= 223 corrected number of grids= 343 volume estimate= 3.15 A**3 Formal charge= -1.0
Pocket contact residues: 62 THR 122 ALA 141 PHE 149 GLU 150 ILE 151 LEU
Pocket contact atoms: 1163 OE1 GLU 1165 N ILE 1173 N LEU 1180 CD2 LEU 1177 CB LEU 1102 CZ PHE
1101 CE2 PHE 1170 CG1 ILE 494 OG1 THR 495 CG2 THR 493 CB THR 951 CB ALA 1157 CA GLU 1160 CB GLU
Pocket 52 subcluster 2 residue= 292 resname=PCK chainid=S
reduced number of grids= 3 corrected number of grids= 9 volume estimate= 0.08 A**3 Formal charge= -1.0
Pocket contact residues: 149 GLU 151 LEU
Pocket contact atoms: 1160 CB GLU 1163 OE1 GLU 1173 N LEU 1177 CB LEU 1101 CE2 PHE 1102 CZ PHE
1165 N ILE 1157 CA GLU 1158 C GLU
Pocket 52 subcluster 3 residue= 293 resname=PCK chainid=S
reduced number of grids= 4 corrected number of grids= 12 volume estimate= 0.11 A**3 Formal charge= -1.0
Pocket contact residues: 141 PHE 149 GLU 151 LEU 152 PRO
Pocket contact atoms: 1101 CE2 PHE 1160 CB GLU 1163 OE1 GLU 1165 N ILE 1173 N LEU 1177 CB LEU
1187 CD PRO 1102 CZ PHE 1157 CA GLU
Pocket 52 subcluster 4 residue= 294 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 3 volume estimate= 0.03 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms: 1102 CZ PHE 1163 OE1 GLU 1177 CB LEU 1180 CD2 LEU 1101 CE2 PHE
Pocket 52 subcluster 5 residue= 295 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 6 volume estimate= 0.06 A**3 Formal charge= 0.0
Pocket contact residues: 62 THR 122 ALA
Pocket contact atoms: 493 CB THR 495 CG2 THR 951 CB ALA 1180 CD2 LEU 948 CA ALA
Pocket 52 subcluster 6 residue= 296 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 4 volume estimate= 0.04 A**3 Formal charge= 0.0
Pocket contact residues: 122 ALA
Pocket contact atoms: 495 CG2 THR 948 CA ALA 951 CB ALA 493 CB THR
Pocket 89 original number of gridpoints= 118 number of gridpoints left after shaving= 51
Number of subclusters= 72 number of subclusters dropped= 67
Pocket 89 subcluster 1 residue= 297 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 9 volume estimate= 0.08 A**3 Formal charge= 0.0
Pocket contact residues: 97 TYR 98 VAL
Pocket contact atoms: 775 CA TYR 778 CB TYR 786 N VAL 976 CD1 LEU 779 CG TYR 781 CD2 TYR
776 C TYR
Pocket 89 subcluster 2 residue= 298 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 10 volume estimate= 0.09 A**3 Formal charge= 0.0
Pocket contact residues: 98 VAL 125 LEU
Pocket contact atoms: 786 N VAL 976 CD1 LEU 775 CA TYR 778 CB TYR 776 C TYR 789 O VAL
925 O THR
Pocket 89 subcluster 3 residue= 299 resname=PCK chainid=S
reduced number of grids= 46 corrected number of grids= 88 volume estimate= 0.81 A**3 Formal charge= 0.0
Pocket contact residues: 98 VAL 118 THR 125 LEU
Pocket contact atoms: 789 O VAL 786 N VAL 925 O THR 976 CD1 LEU 788 C VAL 975 CG LEU
977 CD2 LEU 799 CG2 VAL 933 CB CYS 974 CB LEU 934 SG CYS 929 N CYS
Pocket 89 subcluster 4 residue= 300 resname=PCK chainid=S
reduced number of grids= 2 corrected number of grids= 6 volume estimate= 0.06 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms: 788 C VAL 789 O VAL 799 CG2 VAL 975 CG LEU 976 CD1 LEU 977 CD2 LEU
974 CB LEU 786 N VAL
Pocket 89 subcluster 5 residue= 301 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 5 volume estimate= 0.05 A**3 Formal charge= 0.0
Pocket contact residues:
Pocket contact atoms: 786 N VAL 788 C VAL 789 O VAL 975 CG LEU 976 CD1 LEU 977 CD2 LEU
799 CG2 VAL 787 CA VAL
Pocket 95 original number of gridpoints= 331 number of gridpoints left after shaving= 202
Number of subclusters= 134 number of subclusters dropped= 129
Pocket 95 subcluster 1 residue= 302 resname=PCK chainid=S
reduced number of grids= 195 corrected number of grids= 302 volume estimate= 2.77 A**3 Formal charge= 1.0
Pocket contact residues: 47 SER 50 LEU 51 SER 74 LEU 79 LYS 87 LEU
Pocket contact atoms: 371 O SER 406 CB SER 620 CB LYS 621 CG LYS 694 CD1 LEU 581 CD2 LEU
396 CB LEU 402 N SER 403 CA SER 394 C LEU 369 CA SER 372 CB SER 370 C SER 395 O LEU
622 CD LYS
Pocket 95 subcluster 2 residue= 303 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 6 volume estimate= 0.06 A**3 Formal charge= 1.0
Pocket contact residues: 47 SER 74 LEU 79 LYS
Pocket contact atoms: 369 CA SER 371 O SER 372 CB SER 581 CD2 LEU 621 CG LYS
Pocket 95 subcluster 3 residue= 304 resname=PCK chainid=S
reduced number of grids= 2 corrected number of grids= 6 volume estimate= 0.06 A**3 Formal charge= 0.0
Pocket contact residues: 74 LEU 87 LEU
Pocket contact atoms: 394 C LEU 396 CB LEU 581 CD2 LEU 694 CD1 LEU 395 O LEU
Pocket 95 subcluster 4 residue= 305 resname=PCK chainid=S
reduced number of grids= 1 corrected number of grids= 3 volume estimate= 0.03 A**3 Formal charge= 0.0
Pocket contact residues: 74 LEU
Pocket contact atoms: 396 CB LEU 581 CD2 LEU 694 CD1 LEU
Pocket 95 subcluster 5 residue= 306 resname=PCK chainid=S
reduced number of grids= 3 corrected number of grids= 14 volume estimate= 0.13 A**3 Formal charge= 0.0
Pocket contact residues: 50 LEU 74 LEU 83 TRP 87 LEU
Pocket contact atoms: 581 CD2 LEU 658 CE3 TRP 694 CD1 LEU 395 O LEU 396 CB LEU 660 CZ3 TRP
398 CD1 LEU 394 C LEU
+++++ Closing unit 10
MMC> Input line 19 : STOP NOSF
Date: Tue Jul 20 05:33:38 2010
Unix hostname: atlas.physbio.mssm.edu
Unix directory: /hosts/atlas/homes/mezei/.www/mmc/examples
CPU time: 0 days, 0 hours, 5 minutes, 32 seconds (system time= 18.38 seconds)
----- at least 4 WARNING messages were issued
>>>>> at least 3 OVERRIDE messages were issued
===== at least 1 STRONG WARNING messages were issued
Normal termination at nMC= 0