Starting phenix.real_space_refine (version: dev) on Sat Feb 25 12:09:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgg_34738/02_2023/8hgg_34738.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgg_34738/02_2023/8hgg_34738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgg_34738/02_2023/8hgg_34738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgg_34738/02_2023/8hgg_34738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgg_34738/02_2023/8hgg_34738.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hgg_34738/02_2023/8hgg_34738.pdb" } resolution = 3.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "C PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 25404 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1101 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "B" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1101 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain: "C" Number of atoms: 11600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1484, 11600 Classifications: {'peptide': 1484} Link IDs: {'PTRANS': 97, 'TRANS': 1386} Chain breaks: 3 Chain: "D" Number of atoms: 11600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1484, 11600 Classifications: {'peptide': 1484} Link IDs: {'PTRANS': 97, 'TRANS': 1386} Chain breaks: 3 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.59, per 1000 atoms: 0.57 Number of scatterers: 25404 At special positions: 0 Unit cell: (247.22, 160.956, 124.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 220 16.00 O 4812 8.00 N 4454 7.00 C 15916 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=82, symmetry=0 Simple disulfide: pdb=" SG CYS A 89 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 107 " distance=2.04 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS D 652 " distance=2.03 Simple disulfide: pdb=" SG CYS A 197 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 89 " - pdb=" SG CYS B 128 " distance=2.03 Simple disulfide: pdb=" SG CYS B 104 " - pdb=" SG CYS B 107 " distance=2.04 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS C 652 " distance=2.03 Simple disulfide: pdb=" SG CYS B 197 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 247 " - pdb=" SG CYS C 507 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 577 " distance=2.02 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 360 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 405 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 532 " - pdb=" SG CYS C 563 " distance=2.03 Simple disulfide: pdb=" SG CYS C 630 " - pdb=" SG CYS C 801 " distance=2.03 Simple disulfide: pdb=" SG CYS C 633 " - pdb=" SG CYS C 798 " distance=2.03 Simple disulfide: pdb=" SG CYS C 673 " - pdb=" SG CYS C 755 " distance=2.03 Simple disulfide: pdb=" SG CYS C 695 " - pdb=" SG CYS C 701 " distance=2.03 Simple disulfide: pdb=" SG CYS C 867 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 880 " - pdb=" SG CYS C 891 " distance=2.03 Simple disulfide: pdb=" SG CYS C 903 " - pdb=" SG CYS C 910 " distance=2.04 Simple disulfide: pdb=" SG CYS C 919 " - pdb=" SG CYS C 931 " distance=2.03 Simple disulfide: pdb=" SG CYS C 956 " - pdb=" SG CYS C 990 " distance=2.03 Simple disulfide: pdb=" SG CYS C 971 " - pdb=" SG CYS C1059 " distance=2.03 Simple disulfide: pdb=" SG CYS C1135 " - pdb=" SG CYS C1189 " distance=2.03 Simple disulfide: pdb=" SG CYS C1147 " - pdb=" SG CYS C1158 " distance=2.03 Simple disulfide: pdb=" SG CYS C1162 " - pdb=" SG CYS C1200 " distance=2.03 Simple disulfide: pdb=" SG CYS C1205 " - pdb=" SG CYS C1249 " distance=2.03 Simple disulfide: pdb=" SG CYS C1220 " - pdb=" SG CYS C1230 " distance=2.03 Simple disulfide: pdb=" SG CYS C1234 " - pdb=" SG CYS C1262 " distance=2.03 Simple disulfide: pdb=" SG CYS C1266 " - pdb=" SG CYS C1319 " distance=2.03 Simple disulfide: pdb=" SG CYS C1282 " - pdb=" SG CYS C1293 " distance=2.03 Simple disulfide: pdb=" SG CYS C1297 " - pdb=" SG CYS C1330 " distance=2.03 Simple disulfide: pdb=" SG CYS C1335 " - pdb=" SG CYS C1378 " distance=2.03 Simple disulfide: pdb=" SG CYS C1348 " - pdb=" SG CYS C1358 " distance=2.03 Simple disulfide: pdb=" SG CYS C1412 " - pdb=" SG CYS C1422 " distance=2.03 Simple disulfide: pdb=" SG CYS C1426 " - pdb=" SG CYS C1474 " distance=2.04 Simple disulfide: pdb=" SG CYS C1478 " - pdb=" SG CYS C1496 " distance=2.03 Simple disulfide: pdb=" SG CYS C1487 " - pdb=" SG CYS C1503 " distance=2.03 Simple disulfide: pdb=" SG CYS C1504 " - pdb=" SG CYS C1528 " distance=2.03 Simple disulfide: pdb=" SG CYS C1520 " - pdb=" SG CYS C1526 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 155 " distance=2.03 Simple disulfide: pdb=" SG CYS D 247 " - pdb=" SG CYS D 507 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 577 " distance=2.02 Simple disulfide: pdb=" SG CYS D 334 " - pdb=" SG CYS D 348 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 360 " distance=2.03 Simple disulfide: pdb=" SG CYS D 377 " - pdb=" SG CYS D 393 " distance=2.03 Simple disulfide: pdb=" SG CYS D 394 " - pdb=" SG CYS D 405 " distance=2.03 Simple disulfide: pdb=" SG CYS D 503 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 532 " - pdb=" SG CYS D 563 " distance=2.03 Simple disulfide: pdb=" SG CYS D 630 " - pdb=" SG CYS D 801 " distance=2.03 Simple disulfide: pdb=" SG CYS D 633 " - pdb=" SG CYS D 798 " distance=2.03 Simple disulfide: pdb=" SG CYS D 673 " - pdb=" SG CYS D 755 " distance=2.03 Simple disulfide: pdb=" SG CYS D 695 " - pdb=" SG CYS D 701 " distance=2.03 Simple disulfide: pdb=" SG CYS D 867 " - pdb=" SG CYS D 895 " distance=2.03 Simple disulfide: pdb=" SG CYS D 880 " - pdb=" SG CYS D 891 " distance=2.03 Simple disulfide: pdb=" SG CYS D 903 " - pdb=" SG CYS D 910 " distance=2.03 Simple disulfide: pdb=" SG CYS D 919 " - pdb=" SG CYS D 931 " distance=2.03 Simple disulfide: pdb=" SG CYS D 956 " - pdb=" SG CYS D 990 " distance=2.03 Simple disulfide: pdb=" SG CYS D 971 " - pdb=" SG CYS D1059 " distance=2.03 Simple disulfide: pdb=" SG CYS D1135 " - pdb=" SG CYS D1189 " distance=2.03 Simple disulfide: pdb=" SG CYS D1147 " - pdb=" SG CYS D1158 " distance=2.03 Simple disulfide: pdb=" SG CYS D1162 " - pdb=" SG CYS D1200 " distance=2.03 Simple disulfide: pdb=" SG CYS D1205 " - pdb=" SG CYS D1249 " distance=2.03 Simple disulfide: pdb=" SG CYS D1220 " - pdb=" SG CYS D1230 " distance=2.03 Simple disulfide: pdb=" SG CYS D1234 " - pdb=" SG CYS D1262 " distance=2.03 Simple disulfide: pdb=" SG CYS D1266 " - pdb=" SG CYS D1319 " distance=2.03 Simple disulfide: pdb=" SG CYS D1282 " - pdb=" SG CYS D1293 " distance=2.03 Simple disulfide: pdb=" SG CYS D1297 " - pdb=" SG CYS D1330 " distance=2.03 Simple disulfide: pdb=" SG CYS D1335 " - pdb=" SG CYS D1378 " distance=2.03 Simple disulfide: pdb=" SG CYS D1348 " - pdb=" SG CYS D1358 " distance=2.03 Simple disulfide: pdb=" SG CYS D1412 " - pdb=" SG CYS D1422 " distance=2.03 Simple disulfide: pdb=" SG CYS D1426 " - pdb=" SG CYS D1474 " distance=2.04 Simple disulfide: pdb=" SG CYS D1478 " - pdb=" SG CYS D1496 " distance=2.03 Simple disulfide: pdb=" SG CYS D1487 " - pdb=" SG CYS D1503 " distance=2.03 Simple disulfide: pdb=" SG CYS D1504 " - pdb=" SG CYS D1528 " distance=2.03 Simple disulfide: pdb=" SG CYS D1520 " - pdb=" SG CYS D1526 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.87 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1601 " pdb="ZN ZN C1601 " - pdb=" NE2 HIS C 492 " pdb="ZN ZN C1601 " - pdb=" NE2 HIS C 482 " pdb="ZN ZN C1601 " - pdb=" NE2 HIS C 486 " pdb=" ZN D1601 " pdb="ZN ZN D1601 " - pdb=" NE2 HIS D 492 " pdb="ZN ZN D1601 " - pdb=" NE2 HIS D 482 " pdb="ZN ZN D1601 " - pdb=" NE2 HIS D 486 " 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6024 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 45 sheets defined 12.6% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.781A pdb=" N ASN A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.777A pdb=" N ASN B 142 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 153 removed outlier: 3.541A pdb=" N GLN C 153 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 250 through 253 Processing helix chain 'C' and resid 254 through 264 removed outlier: 3.853A pdb=" N SER C 260 " --> pdb=" O GLU C 256 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR C 261 " --> pdb=" O VAL C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 306 Processing helix chain 'C' and resid 322 through 328 removed outlier: 3.562A pdb=" N ARG C 327 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.672A pdb=" N ILE C 339 " --> pdb=" O ILE C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 358 removed outlier: 3.655A pdb=" N GLY C 357 " --> pdb=" O THR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 391 removed outlier: 4.012A pdb=" N GLY C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 391 " --> pdb=" O ASN C 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 386 through 391' Processing helix chain 'C' and resid 400 through 405 removed outlier: 3.586A pdb=" N THR C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 418 through 426 removed outlier: 3.803A pdb=" N ASN C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 478 through 488 Processing helix chain 'C' and resid 492 through 496 removed outlier: 4.273A pdb=" N GLY C 496 " --> pdb=" O VAL C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 582 Processing helix chain 'C' and resid 815 through 821 removed outlier: 3.539A pdb=" N ILE C 821 " --> pdb=" O ASP C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 877 removed outlier: 3.621A pdb=" N GLN C 876 " --> pdb=" O GLN C 873 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 924 removed outlier: 3.824A pdb=" N GLN C 924 " --> pdb=" O GLU C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 981 through 985 removed outlier: 3.842A pdb=" N GLN C 984 " --> pdb=" O GLY C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 Processing helix chain 'C' and resid 1105 through 1110 removed outlier: 3.726A pdb=" N SER C1110 " --> pdb=" O PRO C1106 " (cutoff:3.500A) Processing helix chain 'C' and resid 1280 through 1284 removed outlier: 3.522A pdb=" N GLU C1284 " --> pdb=" O ARG C1281 " (cutoff:3.500A) Processing helix chain 'C' and resid 1339 through 1343 Processing helix chain 'C' and resid 1493 through 1495 No H-bonds generated for 'chain 'C' and resid 1493 through 1495' Processing helix chain 'C' and resid 1496 through 1502 removed outlier: 3.502A pdb=" N ASP C1502 " --> pdb=" O TYR C1498 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 removed outlier: 3.537A pdb=" N GLN D 153 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 194 Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 254 through 264 removed outlier: 3.827A pdb=" N SER D 260 " --> pdb=" O GLU D 256 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR D 261 " --> pdb=" O VAL D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 306 Processing helix chain 'D' and resid 322 through 328 removed outlier: 3.566A pdb=" N ARG D 327 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG D 328 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.670A pdb=" N ILE D 339 " --> pdb=" O ILE D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 358 removed outlier: 3.687A pdb=" N GLY D 357 " --> pdb=" O THR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 391 removed outlier: 4.030A pdb=" N GLY D 390 " --> pdb=" O PHE D 386 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY D 391 " --> pdb=" O ASN D 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 386 through 391' Processing helix chain 'D' and resid 400 through 405 removed outlier: 3.598A pdb=" N THR D 404 " --> pdb=" O ASN D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 426 removed outlier: 3.796A pdb=" N ASN D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 424 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 471 Processing helix chain 'D' and resid 478 through 488 Processing helix chain 'D' and resid 492 through 496 removed outlier: 4.285A pdb=" N GLY D 496 " --> pdb=" O VAL D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 582 Processing helix chain 'D' and resid 815 through 821 removed outlier: 3.544A pdb=" N ILE D 821 " --> pdb=" O ASP D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 873 through 877 removed outlier: 3.628A pdb=" N GLN D 876 " --> pdb=" O GLN D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 924 removed outlier: 3.779A pdb=" N GLN D 924 " --> pdb=" O GLU D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 981 through 985 removed outlier: 3.843A pdb=" N GLN D 984 " --> pdb=" O GLY D 981 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 1000 Processing helix chain 'D' and resid 1105 through 1110 removed outlier: 3.719A pdb=" N SER D1110 " --> pdb=" O PRO D1106 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1284 removed outlier: 3.517A pdb=" N GLU D1284 " --> pdb=" O ARG D1281 " (cutoff:3.500A) Processing helix chain 'D' and resid 1339 through 1343 removed outlier: 3.625A pdb=" N HIS D1343 " --> pdb=" O PRO D1340 " (cutoff:3.500A) Processing helix chain 'D' and resid 1493 through 1495 No H-bonds generated for 'chain 'D' and resid 1493 through 1495' Processing helix chain 'D' and resid 1496 through 1501 removed outlier: 3.520A pdb=" N GLY D1500 " --> pdb=" O CYS D1496 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 98 removed outlier: 5.626A pdb=" N SER A 114 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU A 216 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 174 removed outlier: 3.758A pdb=" N ILE A 159 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N VAL A 198 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 95 through 98 removed outlier: 5.626A pdb=" N SER B 114 " --> pdb=" O LEU B 216 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU B 216 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 172 through 174 removed outlier: 3.754A pdb=" N ILE B 159 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL B 198 " --> pdb=" O ILE B 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 135 through 140 removed outlier: 5.413A pdb=" N GLN C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL C 132 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 138 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 135 through 140 removed outlier: 5.413A pdb=" N GLN C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL C 132 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 138 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS C 227 " --> pdb=" O TYR C 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 103 through 106 removed outlier: 3.566A pdb=" N TRP C 73 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE C 77 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N VAL C 56 " --> pdb=" O ILE C 77 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 311 through 321 removed outlier: 5.154A pdb=" N PHE C 437 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU C 280 " --> pdb=" O PHE C 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 329 through 331 removed outlier: 5.893A pdb=" N LEU C 329 " --> pdb=" O LEU C 416 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 600 through 604 removed outlier: 5.217A pdb=" N VAL C 601 " --> pdb=" O GLU C 612 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU C 612 " --> pdb=" O VAL C 601 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY C 603 " --> pdb=" O THR C 610 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 609 " --> pdb=" O ASP C 830 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP C 830 " --> pdb=" O VAL C 609 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 640 through 642 removed outlier: 6.572A pdb=" N GLU C 783 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N TRP C 719 " --> pdb=" O ASP C 785 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA C 787 " --> pdb=" O THR C 717 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 717 " --> pdb=" O ALA C 787 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU C 789 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER C 715 " --> pdb=" O LEU C 789 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER C 791 " --> pdb=" O PRO C 713 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 645 through 647 removed outlier: 6.163A pdb=" N TYR C 771 " --> pdb=" O PHE C 707 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY C 772 " --> pdb=" O LEU C 739 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 735 " --> pdb=" O TYR C 776 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE C 736 " --> pdb=" O LEU C 748 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 805 through 810 Processing sheet with id=AB5, first strand: chain 'C' and resid 901 through 903 Processing sheet with id=AB6, first strand: chain 'C' and resid 939 through 943 removed outlier: 5.688A pdb=" N VAL C1091 " --> pdb=" O ASP C1026 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASP C1026 " --> pdb=" O VAL C1091 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE C1093 " --> pdb=" O VAL C1024 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N VAL C1024 " --> pdb=" O ILE C1093 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C1095 " --> pdb=" O HIS C1022 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C1018 " --> pdb=" O ARG C1099 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 945 through 949 removed outlier: 4.989A pdb=" N ASN C 946 " --> pdb=" O TYR C1009 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR C1009 " --> pdb=" O ASN C 946 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N ALA C1008 " --> pdb=" O SER C1085 " (cutoff:3.500A) removed outlier: 10.967A pdb=" N SER C1085 " --> pdb=" O ALA C1008 " (cutoff:3.500A) removed outlier: 12.371A pdb=" N PHE C1010 " --> pdb=" O ARG C1083 " (cutoff:3.500A) removed outlier: 11.896A pdb=" N ARG C1083 " --> pdb=" O PHE C1010 " (cutoff:3.500A) removed outlier: 11.308A pdb=" N GLN C1012 " --> pdb=" O ALA C1081 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N ALA C1081 " --> pdb=" O GLN C1012 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET C1014 " --> pdb=" O SER C1079 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL C1040 " --> pdb=" O GLY C1053 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY C1053 " --> pdb=" O VAL C1040 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU C1042 " --> pdb=" O ASP C1051 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASP C1051 " --> pdb=" O LEU C1042 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ASP C1044 " --> pdb=" O SER C1049 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N SER C1049 " --> pdb=" O ASP C1044 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 1069 through 1071 Processing sheet with id=AB9, first strand: chain 'C' and resid 1143 through 1147 Processing sheet with id=AC1, first strand: chain 'C' and resid 1175 through 1176 removed outlier: 3.641A pdb=" N ALA C1199 " --> pdb=" O GLN C1169 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1216 through 1219 Processing sheet with id=AC3, first strand: chain 'C' and resid 1238 through 1242 Processing sheet with id=AC4, first strand: chain 'C' and resid 1275 through 1277 Processing sheet with id=AC5, first strand: chain 'C' and resid 1346 through 1348 Processing sheet with id=AC6, first strand: chain 'C' and resid 1408 through 1411 Processing sheet with id=AC7, first strand: chain 'C' and resid 1431 through 1435 Processing sheet with id=AC8, first strand: chain 'D' and resid 135 through 140 removed outlier: 5.421A pdb=" N GLN D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 132 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 138 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 135 through 140 removed outlier: 5.421A pdb=" N GLN D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D 132 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA D 138 " --> pdb=" O LEU D 130 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS D 227 " --> pdb=" O TYR D 18 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 103 through 106 removed outlier: 3.568A pdb=" N TRP D 73 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE D 77 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL D 56 " --> pdb=" O ILE D 77 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N LEU D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 311 through 321 removed outlier: 5.141A pdb=" N PHE D 437 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N LEU D 280 " --> pdb=" O PHE D 437 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 329 through 331 removed outlier: 5.877A pdb=" N LEU D 329 " --> pdb=" O LEU D 416 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 600 through 604 removed outlier: 5.221A pdb=" N VAL D 601 " --> pdb=" O GLU D 612 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU D 612 " --> pdb=" O VAL D 601 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY D 603 " --> pdb=" O THR D 610 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 609 " --> pdb=" O ASP D 830 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP D 830 " --> pdb=" O VAL D 609 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 640 through 642 removed outlier: 6.584A pdb=" N GLU D 783 " --> pdb=" O THR D 721 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N TRP D 719 " --> pdb=" O ASP D 785 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA D 787 " --> pdb=" O THR D 717 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR D 717 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU D 789 " --> pdb=" O SER D 715 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N SER D 715 " --> pdb=" O LEU D 789 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER D 791 " --> pdb=" O PRO D 713 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 645 through 647 removed outlier: 6.171A pdb=" N TYR D 771 " --> pdb=" O PHE D 707 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY D 772 " --> pdb=" O LEU D 739 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP D 735 " --> pdb=" O TYR D 776 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE D 736 " --> pdb=" O LEU D 748 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 805 through 810 Processing sheet with id=AD8, first strand: chain 'D' and resid 901 through 903 Processing sheet with id=AD9, first strand: chain 'D' and resid 939 through 943 removed outlier: 5.666A pdb=" N VAL D1091 " --> pdb=" O ASP D1026 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ASP D1026 " --> pdb=" O VAL D1091 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE D1093 " --> pdb=" O VAL D1024 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL D1024 " --> pdb=" O ILE D1093 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D1095 " --> pdb=" O HIS D1022 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA D1018 " --> pdb=" O ARG D1099 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 945 through 949 removed outlier: 4.987A pdb=" N ASN D 946 " --> pdb=" O TYR D1009 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N TYR D1009 " --> pdb=" O ASN D 946 " (cutoff:3.500A) removed outlier: 11.983A pdb=" N ALA D1008 " --> pdb=" O SER D1085 " (cutoff:3.500A) removed outlier: 10.964A pdb=" N SER D1085 " --> pdb=" O ALA D1008 " (cutoff:3.500A) removed outlier: 12.337A pdb=" N PHE D1010 " --> pdb=" O ARG D1083 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ARG D1083 " --> pdb=" O PHE D1010 " (cutoff:3.500A) removed outlier: 11.273A pdb=" N GLN D1012 " --> pdb=" O ALA D1081 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ALA D1081 " --> pdb=" O GLN D1012 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET D1014 " --> pdb=" O SER D1079 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL D1040 " --> pdb=" O GLY D1053 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY D1053 " --> pdb=" O VAL D1040 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU D1042 " --> pdb=" O ASP D1051 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ASP D1051 " --> pdb=" O LEU D1042 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ASP D1044 " --> pdb=" O SER D1049 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER D1049 " --> pdb=" O ASP D1044 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1143 through 1147 Processing sheet with id=AE3, first strand: chain 'D' and resid 1175 through 1176 removed outlier: 3.646A pdb=" N ALA D1199 " --> pdb=" O GLN D1169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1216 through 1219 Processing sheet with id=AE5, first strand: chain 'D' and resid 1239 through 1242 removed outlier: 3.760A pdb=" N LYS D1241 " --> pdb=" O LEU D1261 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1275 through 1277 Processing sheet with id=AE7, first strand: chain 'D' and resid 1346 through 1348 Processing sheet with id=AE8, first strand: chain 'D' and resid 1408 through 1411 Processing sheet with id=AE9, first strand: chain 'D' and resid 1431 through 1435 592 hydrogen bonds defined for protein. 1572 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.16 Time building geometry restraints manager: 10.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8173 1.34 - 1.46: 6090 1.46 - 1.58: 11569 1.58 - 1.71: 0 1.71 - 1.83: 264 Bond restraints: 26096 Sorted by residual: bond pdb=" N ILE C1066 " pdb=" CA ILE C1066 " ideal model delta sigma weight residual 1.458 1.489 -0.031 7.70e-03 1.69e+04 1.61e+01 bond pdb=" N TYR D1466 " pdb=" CA TYR D1466 " ideal model delta sigma weight residual 1.462 1.489 -0.026 7.70e-03 1.69e+04 1.18e+01 bond pdb=" N ILE D1472 " pdb=" CA ILE D1472 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.10e-02 8.26e+03 1.03e+01 bond pdb=" N TYR C1466 " pdb=" CA TYR C1466 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.07e+00 bond pdb=" N TRP C1465 " pdb=" CA TRP C1465 " ideal model delta sigma weight residual 1.456 1.490 -0.033 1.21e-02 6.83e+03 7.57e+00 ... (remaining 26091 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.82: 1058 106.82 - 113.69: 14064 113.69 - 120.56: 9824 120.56 - 127.43: 10170 127.43 - 134.30: 402 Bond angle restraints: 35518 Sorted by residual: angle pdb=" CA MET C 473 " pdb=" C MET C 473 " pdb=" O MET C 473 " ideal model delta sigma weight residual 120.19 116.81 3.38 9.30e-01 1.16e+00 1.32e+01 angle pdb=" CA MET D 473 " pdb=" C MET D 473 " pdb=" O MET D 473 " ideal model delta sigma weight residual 120.19 116.83 3.36 9.30e-01 1.16e+00 1.30e+01 angle pdb=" N PRO C1467 " pdb=" CA PRO C1467 " pdb=" C PRO C1467 " ideal model delta sigma weight residual 112.47 105.16 7.31 2.06e+00 2.36e-01 1.26e+01 angle pdb=" C GLU D 442 " pdb=" N GLU D 443 " pdb=" CA GLU D 443 " ideal model delta sigma weight residual 122.61 127.93 -5.32 1.56e+00 4.11e-01 1.16e+01 angle pdb=" C GLU C 442 " pdb=" N GLU C 443 " pdb=" CA GLU C 443 " ideal model delta sigma weight residual 122.61 127.92 -5.31 1.56e+00 4.11e-01 1.16e+01 ... (remaining 35513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.50: 14044 13.50 - 26.99: 1183 26.99 - 40.49: 348 40.49 - 53.98: 121 53.98 - 67.48: 34 Dihedral angle restraints: 15730 sinusoidal: 6366 harmonic: 9364 Sorted by residual: dihedral pdb=" CB CYS B 104 " pdb=" SG CYS B 104 " pdb=" SG CYS B 107 " pdb=" CB CYS B 107 " ideal model delta sinusoidal sigma weight residual 93.00 153.21 -60.21 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CB CYS A 104 " pdb=" SG CYS A 104 " pdb=" SG CYS A 107 " pdb=" CB CYS A 107 " ideal model delta sinusoidal sigma weight residual 93.00 153.18 -60.18 1 1.00e+01 1.00e-02 4.83e+01 dihedral pdb=" CB CYS D 252 " pdb=" SG CYS D 252 " pdb=" SG CYS D 577 " pdb=" CB CYS D 577 " ideal model delta sinusoidal sigma weight residual 93.00 152.44 -59.44 1 1.00e+01 1.00e-02 4.72e+01 ... (remaining 15727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2860 0.049 - 0.098: 684 0.098 - 0.147: 224 0.147 - 0.196: 23 0.196 - 0.245: 3 Chirality restraints: 3794 Sorted by residual: chirality pdb=" CA ILE C1065 " pdb=" N ILE C1065 " pdb=" C ILE C1065 " pdb=" CB ILE C1065 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA LEU C1064 " pdb=" N LEU C1064 " pdb=" C LEU C1064 " pdb=" CB LEU C1064 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE C1066 " pdb=" N ILE C1066 " pdb=" C ILE C1066 " pdb=" CB ILE C1066 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 3791 not shown) Planarity restraints: 4686 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C1062 " -0.011 2.00e-02 2.50e+03 2.18e-02 4.76e+00 pdb=" C ASN C1062 " 0.038 2.00e-02 2.50e+03 pdb=" O ASN C1062 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO C1063 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 988 " -0.036 5.00e-02 4.00e+02 5.42e-02 4.70e+00 pdb=" N PRO C 989 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 989 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 989 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 988 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO D 989 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 989 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 989 " -0.030 5.00e-02 4.00e+02 ... (remaining 4683 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7236 2.82 - 3.34: 20066 3.34 - 3.86: 41875 3.86 - 4.38: 47884 4.38 - 4.90: 83610 Nonbonded interactions: 200671 Sorted by model distance: nonbonded pdb=" OD1 ASP D 87 " pdb=" OG SER D 110 " model vdw 2.296 2.440 nonbonded pdb=" OD1 ASP C 87 " pdb=" OG SER C 110 " model vdw 2.299 2.440 nonbonded pdb=" OE1 GLN B 156 " pdb=" OH TYR D1486 " model vdw 2.308 2.440 nonbonded pdb=" O HIS B 188 " pdb=" OG SER B 192 " model vdw 2.327 2.440 nonbonded pdb=" O ASN C 400 " pdb=" OG1 THR C 404 " model vdw 2.327 2.440 ... (remaining 200666 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 220 5.16 5 C 15916 2.51 5 N 4454 2.21 5 O 4812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 5.940 Check model and map are aligned: 0.400 Process input model: 73.490 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.220 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 26096 Z= 0.231 Angle : 0.619 8.596 35518 Z= 0.339 Chirality : 0.048 0.245 3794 Planarity : 0.006 0.054 4686 Dihedral : 11.942 67.476 9460 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.42 % Favored : 96.55 % Rotamer Outliers : 5.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3218 helix: -2.74 (0.20), residues: 288 sheet: 0.26 (0.20), residues: 676 loop : -1.08 (0.12), residues: 2254 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 390 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 155 outliers final: 48 residues processed: 516 average time/residue: 0.3778 time to fit residues: 311.9544 Evaluate side-chains 283 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 235 time to evaluate : 2.884 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.2420 time to fit residues: 25.9507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 164 optimal weight: 0.0030 chunk 130 optimal weight: 0.3980 chunk 252 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 187 optimal weight: 2.9990 chunk 292 optimal weight: 30.0000 overall best weight: 1.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN A 173 GLN B 116 GLN B 156 GLN C 294 GLN C 374 ASN C 403 GLN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 ASN C 683 ASN C 985 HIS D 153 GLN D 294 GLN ** D 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN D 403 GLN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN D 587 GLN D 683 ASN D 985 HIS D1062 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 26096 Z= 0.197 Angle : 0.531 6.815 35518 Z= 0.275 Chirality : 0.044 0.155 3794 Planarity : 0.005 0.068 4686 Dihedral : 4.487 23.264 3496 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3218 helix: -1.55 (0.26), residues: 302 sheet: 0.18 (0.21), residues: 656 loop : -0.83 (0.12), residues: 2260 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 256 time to evaluate : 2.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 26 residues processed: 305 average time/residue: 0.3397 time to fit residues: 173.3338 Evaluate side-chains 250 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 224 time to evaluate : 3.029 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.2604 time to fit residues: 17.0989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 243 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 292 optimal weight: 20.0000 chunk 316 optimal weight: 10.0000 chunk 260 optimal weight: 4.9990 chunk 290 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 235 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 142 ASN A 156 GLN B 116 GLN B 142 ASN B 156 GLN C 78 HIS C 153 GLN C 362 HIS C 365 HIS C 374 ASN C 478 HIS ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 587 GLN C 687 ASN ** C 969 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 GLN D 78 HIS D 362 HIS D 365 HIS D 374 ASN D 478 HIS ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 ASN D 969 GLN D1048 GLN D1318 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 26096 Z= 0.471 Angle : 0.681 7.523 35518 Z= 0.359 Chirality : 0.049 0.200 3794 Planarity : 0.005 0.053 4686 Dihedral : 5.268 25.768 3496 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3218 helix: -1.50 (0.26), residues: 304 sheet: -0.26 (0.20), residues: 650 loop : -1.02 (0.12), residues: 2264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 223 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 48 residues processed: 298 average time/residue: 0.3442 time to fit residues: 171.0902 Evaluate side-chains 255 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 207 time to evaluate : 2.833 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.2354 time to fit residues: 25.0619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 20.0000 chunk 220 optimal weight: 2.9990 chunk 152 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 196 optimal weight: 2.9990 chunk 293 optimal weight: 0.0670 chunk 311 optimal weight: 30.0000 chunk 153 optimal weight: 6.9990 chunk 278 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 142 ASN A 173 GLN B 142 ASN ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 GLN C 333 ASN C 365 HIS C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 687 ASN C1491 ASN D 83 GLN D 365 HIS D 374 ASN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 ASN D 687 ASN D1318 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 26096 Z= 0.215 Angle : 0.538 6.070 35518 Z= 0.280 Chirality : 0.044 0.166 3794 Planarity : 0.004 0.039 4686 Dihedral : 4.799 26.138 3496 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.14), residues: 3218 helix: -0.98 (0.29), residues: 304 sheet: -0.17 (0.21), residues: 662 loop : -0.86 (0.12), residues: 2252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 223 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 21 residues processed: 255 average time/residue: 0.3434 time to fit residues: 147.7702 Evaluate side-chains 228 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2290 time to fit residues: 13.1679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 231 optimal weight: 0.1980 chunk 128 optimal weight: 7.9990 chunk 265 optimal weight: 8.9990 chunk 215 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 158 optimal weight: 30.0000 chunk 279 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 overall best weight: 3.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN B 116 GLN ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 HIS D 374 ASN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1411 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 26096 Z= 0.380 Angle : 0.635 14.233 35518 Z= 0.329 Chirality : 0.047 0.291 3794 Planarity : 0.005 0.044 4686 Dihedral : 5.140 25.210 3496 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 2.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.14), residues: 3218 helix: -1.36 (0.27), residues: 328 sheet: -0.47 (0.21), residues: 652 loop : -1.00 (0.12), residues: 2238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 213 time to evaluate : 3.156 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 32 residues processed: 257 average time/residue: 0.3754 time to fit residues: 161.9214 Evaluate side-chains 234 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 3.106 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2353 time to fit residues: 18.7514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 7.9990 chunk 280 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 311 optimal weight: 30.0000 chunk 258 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN B 116 GLN C 78 HIS C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 GLN D 78 HIS D 333 ASN D 374 ASN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1411 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 26096 Z= 0.269 Angle : 0.571 17.075 35518 Z= 0.293 Chirality : 0.045 0.219 3794 Planarity : 0.004 0.040 4686 Dihedral : 4.935 26.823 3496 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 1.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3218 helix: -1.36 (0.27), residues: 338 sheet: -0.38 (0.20), residues: 662 loop : -0.93 (0.13), residues: 2218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 212 time to evaluate : 3.037 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 16 residues processed: 246 average time/residue: 0.3432 time to fit residues: 143.3857 Evaluate side-chains 215 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 time to evaluate : 2.731 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2919 time to fit residues: 12.1053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 177 optimal weight: 0.8980 chunk 227 optimal weight: 9.9990 chunk 176 optimal weight: 0.6980 chunk 262 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 143 optimal weight: 9.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN C 234 HIS C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1411 GLN D 374 ASN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1411 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 26096 Z= 0.283 Angle : 0.571 8.304 35518 Z= 0.296 Chirality : 0.045 0.293 3794 Planarity : 0.004 0.041 4686 Dihedral : 4.894 23.773 3496 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.14), residues: 3218 helix: -1.21 (0.28), residues: 326 sheet: -0.45 (0.21), residues: 660 loop : -0.93 (0.13), residues: 2232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 206 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 226 average time/residue: 0.3407 time to fit residues: 131.6887 Evaluate side-chains 213 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 2.885 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2343 time to fit residues: 10.9100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 197 optimal weight: 0.5980 chunk 211 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 chunk 243 optimal weight: 0.9980 chunk 282 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 HIS ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1411 GLN ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 26096 Z= 0.151 Angle : 0.503 8.029 35518 Z= 0.258 Chirality : 0.043 0.173 3794 Planarity : 0.004 0.038 4686 Dihedral : 4.448 25.932 3496 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer Outliers : 0.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3218 helix: -1.07 (0.28), residues: 340 sheet: -0.16 (0.21), residues: 640 loop : -0.77 (0.13), residues: 2238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 222 time to evaluate : 2.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 232 average time/residue: 0.3468 time to fit residues: 136.8312 Evaluate side-chains 204 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 200 time to evaluate : 2.945 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2177 time to fit residues: 5.6126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 5.9990 chunk 271 optimal weight: 7.9990 chunk 289 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 88 optimal weight: 0.0980 chunk 261 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 288 optimal weight: 8.9990 chunk 189 optimal weight: 0.7980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1411 GLN D1450 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 26096 Z= 0.308 Angle : 0.568 8.317 35518 Z= 0.294 Chirality : 0.046 0.288 3794 Planarity : 0.004 0.044 4686 Dihedral : 4.730 23.299 3496 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.14), residues: 3218 helix: -1.24 (0.27), residues: 340 sheet: -0.48 (0.21), residues: 662 loop : -0.81 (0.13), residues: 2216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 203 time to evaluate : 3.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 211 average time/residue: 0.3467 time to fit residues: 123.8189 Evaluate side-chains 198 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 192 time to evaluate : 2.921 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2492 time to fit residues: 7.3559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 0.0000 chunk 186 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 chunk 212 optimal weight: 8.9990 chunk 320 optimal weight: 0.4980 chunk 295 optimal weight: 1.9990 chunk 255 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 197 optimal weight: 0.7980 chunk 156 optimal weight: 0.0870 chunk 202 optimal weight: 0.9990 overall best weight: 0.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN C 460 HIS ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 554 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 HIS ** D 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN D1411 GLN ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 26096 Z= 0.137 Angle : 0.493 8.260 35518 Z= 0.252 Chirality : 0.043 0.157 3794 Planarity : 0.004 0.038 4686 Dihedral : 4.262 25.732 3496 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3218 helix: -0.80 (0.29), residues: 328 sheet: -0.09 (0.21), residues: 646 loop : -0.66 (0.13), residues: 2244 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6436 Ramachandran restraints generated. 3218 Oldfield, 0 Emsley, 3218 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 215 time to evaluate : 3.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 217 average time/residue: 0.3403 time to fit residues: 125.3414 Evaluate side-chains 202 residues out of total 2838 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2410 time to fit residues: 4.7016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 chunk 235 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 255 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 262 optimal weight: 0.0070 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 224 optimal weight: 4.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN C 374 ASN ** C 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 587 GLN D1411 GLN ** D1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.197897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.191906 restraints weight = 31964.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.183305 restraints weight = 76914.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.178498 restraints weight = 70506.731| |-----------------------------------------------------------------------------| r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 26096 Z= 0.191 Angle : 0.515 7.496 35518 Z= 0.263 Chirality : 0.043 0.174 3794 Planarity : 0.004 0.038 4686 Dihedral : 4.329 23.161 3496 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3218 helix: -0.88 (0.28), residues: 340 sheet: -0.09 (0.21), residues: 644 loop : -0.66 (0.13), residues: 2234 =============================================================================== Job complete usr+sys time: 4237.73 seconds wall clock time: 79 minutes 10.22 seconds (4750.22 seconds total)