Starting phenix.real_space_refine (version: 1.21rc1) on Fri Aug 25 15:17:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/08_2023/5vkq_8702_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/08_2023/5vkq_8702.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/08_2023/5vkq_8702_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/08_2023/5vkq_8702_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/08_2023/5vkq_8702_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/08_2023/5vkq_8702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/08_2023/5vkq_8702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/08_2023/5vkq_8702_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/08_2023/5vkq_8702_updated.pdb" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= -0.000 sd= 1.000 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 188 5.16 5 C 26900 2.51 5 N 7352 2.21 5 O 7428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A ARG 724": "NH1" <-> "NH2" Residue "A ARG 727": "NH1" <-> "NH2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A ARG 1144": "NH1" <-> "NH2" Residue "A TYR 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1401": "NH1" <-> "NH2" Residue "A ARG 1483": "NH1" <-> "NH2" Residue "A ARG 1581": "NH1" <-> "NH2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B ARG 483": "NH1" <-> "NH2" Residue "B ARG 724": "NH1" <-> "NH2" Residue "B ARG 727": "NH1" <-> "NH2" Residue "B ARG 1127": "NH1" <-> "NH2" Residue "B ARG 1144": "NH1" <-> "NH2" Residue "B TYR 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1401": "NH1" <-> "NH2" Residue "B ARG 1483": "NH1" <-> "NH2" Residue "B ARG 1581": "NH1" <-> "NH2" Residue "C ARG 477": "NH1" <-> "NH2" Residue "C ARG 483": "NH1" <-> "NH2" Residue "C ARG 724": "NH1" <-> "NH2" Residue "C ARG 727": "NH1" <-> "NH2" Residue "C ARG 1127": "NH1" <-> "NH2" Residue "C ARG 1144": "NH1" <-> "NH2" Residue "C TYR 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1401": "NH1" <-> "NH2" Residue "C ARG 1483": "NH1" <-> "NH2" Residue "C ARG 1581": "NH1" <-> "NH2" Residue "D ARG 477": "NH1" <-> "NH2" Residue "D ARG 483": "NH1" <-> "NH2" Residue "D ARG 724": "NH1" <-> "NH2" Residue "D ARG 727": "NH1" <-> "NH2" Residue "D ARG 1127": "NH1" <-> "NH2" Residue "D ARG 1144": "NH1" <-> "NH2" Residue "D TYR 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1401": "NH1" <-> "NH2" Residue "D ARG 1483": "NH1" <-> "NH2" Residue "D ARG 1581": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 41900 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1499, 10217 Classifications: {'peptide': 1499} Incomplete info: {'truncation_to_alanine': 402} Link IDs: {'PTRANS': 47, 'TRANS': 1451} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1364 Unresolved non-hydrogen angles: 1705 Unresolved non-hydrogen dihedrals: 1090 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 51, 'TYR:plan': 6, 'ASN:plan1': 33, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 7, 'GLU:plan': 52, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 809 Chain: "B" Number of atoms: 10217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1499, 10217 Classifications: {'peptide': 1499} Incomplete info: {'truncation_to_alanine': 402} Link IDs: {'PTRANS': 47, 'TRANS': 1451} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1364 Unresolved non-hydrogen angles: 1705 Unresolved non-hydrogen dihedrals: 1090 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 51, 'TYR:plan': 6, 'ASN:plan1': 33, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 7, 'GLU:plan': 52, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 809 Chain: "C" Number of atoms: 10217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1499, 10217 Classifications: {'peptide': 1499} Incomplete info: {'truncation_to_alanine': 402} Link IDs: {'PTRANS': 47, 'TRANS': 1451} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1364 Unresolved non-hydrogen angles: 1705 Unresolved non-hydrogen dihedrals: 1090 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 51, 'TYR:plan': 6, 'ASN:plan1': 33, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 7, 'GLU:plan': 52, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 809 Chain: "D" Number of atoms: 10217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1499, 10217 Classifications: {'peptide': 1499} Incomplete info: {'truncation_to_alanine': 402} Link IDs: {'PTRANS': 47, 'TRANS': 1451} Chain breaks: 1 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 1364 Unresolved non-hydrogen angles: 1705 Unresolved non-hydrogen dihedrals: 1090 Unresolved non-hydrogen chiralities: 97 Planarities with less than four sites: {'GLN:plan1': 18, 'ASP:plan': 51, 'TYR:plan': 6, 'ASN:plan1': 33, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 7, 'GLU:plan': 52, 'ARG:plan': 27} Unresolved non-hydrogen planarities: 809 Chain: "A" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 258 Unusual residues: {'PCF': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 129 Planarities with less than four sites: {'PCF:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 258 Unusual residues: {'PCF': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 129 Planarities with less than four sites: {'PCF:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 258 Unusual residues: {'PCF': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 129 Planarities with less than four sites: {'PCF:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 258 Unusual residues: {'PCF': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 129 Planarities with less than four sites: {'PCF:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 20.88, per 1000 atoms: 0.50 Number of scatterers: 41900 At special positions: 0 Unit cell: (176.262, 176.262, 260.138, 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) S 188 16.00 P 32 15.00 O 7428 8.00 N 7352 7.00 C 26900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 15.92 Conformation dependent library (CDL) restraints added in 7.3 seconds 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11184 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 344 helices and 0 sheets defined 56.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.87 Creating SS restraints... Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 179 through 187 Proline residue: A 187 - end of helix Processing helix chain 'A' and resid 201 through 207 Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 236 through 242 Processing helix chain 'A' and resid 252 through 260 Processing helix chain 'A' and resid 271 through 277 Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 314 through 322 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 348 through 355 Processing helix chain 'A' and resid 372 through 378 Processing helix chain 'A' and resid 381 through 389 removed outlier: 3.800A pdb=" N MET A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 414 through 423 Processing helix chain 'A' and resid 438 through 444 removed outlier: 4.571A pdb=" N GLU A 443 " --> pdb=" O HIS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 456 Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 481 through 490 removed outlier: 4.320A pdb=" N ALA A 485 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU A 486 " --> pdb=" O ARG A 483 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 490 " --> pdb=" O MET A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 515 through 523 Processing helix chain 'A' and resid 538 through 544 Processing helix chain 'A' and resid 548 through 561 removed outlier: 3.730A pdb=" N GLU A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 Processing helix chain 'A' and resid 576 through 578 No H-bonds generated for 'chain 'A' and resid 576 through 578' Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.736A pdb=" N CYS A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 608 Processing helix chain 'A' and resid 624 through 631 removed outlier: 3.682A pdb=" N CYS A 628 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 637 through 643 Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 663 through 670 Processing helix chain 'A' and resid 673 through 681 Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 706 through 714 Processing helix chain 'A' and resid 729 through 736 Processing helix chain 'A' and resid 739 through 749 Processing helix chain 'A' and resid 763 through 770 removed outlier: 3.818A pdb=" N SER A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 782 Processing helix chain 'A' and resid 796 through 802 Processing helix chain 'A' and resid 806 through 814 Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 830 through 837 Processing helix chain 'A' and resid 840 through 855 removed outlier: 8.170A pdb=" N SER A 852 " --> pdb=" O LYS A 848 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY A 853 " --> pdb=" O PHE A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 873 Processing helix chain 'A' and resid 876 through 885 Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 909 through 918 removed outlier: 4.022A pdb=" N THR A 918 " --> pdb=" O VAL A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 938 Processing helix chain 'A' and resid 942 through 951 Processing helix chain 'A' and resid 978 through 985 Processing helix chain 'A' and resid 988 through 996 removed outlier: 3.644A pdb=" N ASN A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1018 Processing helix chain 'A' and resid 1023 through 1032 Processing helix chain 'A' and resid 1047 through 1054 Processing helix chain 'A' and resid 1057 through 1066 Processing helix chain 'A' and resid 1080 through 1087 Processing helix chain 'A' and resid 1090 through 1098 Processing helix chain 'A' and resid 1113 through 1119 Processing helix chain 'A' and resid 1123 through 1131 Processing helix chain 'A' and resid 1136 through 1139 No H-bonds generated for 'chain 'A' and resid 1136 through 1139' Processing helix chain 'A' and resid 1143 through 1155 Processing helix chain 'A' and resid 1159 through 1167 Processing helix chain 'A' and resid 1171 through 1188 removed outlier: 3.653A pdb=" N THR A1187 " --> pdb=" O ILE A1183 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1215 removed outlier: 3.839A pdb=" N VAL A1197 " --> pdb=" O ALA A1193 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A1198 " --> pdb=" O LYS A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1224 Processing helix chain 'A' and resid 1234 through 1240 Processing helix chain 'A' and resid 1244 through 1247 No H-bonds generated for 'chain 'A' and resid 1244 through 1247' Processing helix chain 'A' and resid 1250 through 1261 Processing helix chain 'A' and resid 1270 through 1280 removed outlier: 3.917A pdb=" N VAL A1276 " --> pdb=" O LEU A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1282 through 1289 Processing helix chain 'A' and resid 1300 through 1322 Processing helix chain 'A' and resid 1338 through 1356 Processing helix chain 'A' and resid 1363 through 1386 removed outlier: 4.073A pdb=" N ILE A1367 " --> pdb=" O LEU A1364 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY A1375 " --> pdb=" O LEU A1372 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET A1376 " --> pdb=" O LEU A1373 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL A1379 " --> pdb=" O MET A1376 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL A1383 " --> pdb=" O GLY A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1396 through 1418 Processing helix chain 'A' and resid 1428 through 1461 removed outlier: 3.952A pdb=" N ILE A1433 " --> pdb=" O ALA A1430 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY A1434 " --> pdb=" O ILE A1431 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP A1435 " --> pdb=" O ILE A1432 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP A1439 " --> pdb=" O LEU A1436 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A1440 " --> pdb=" O LEU A1437 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A1445 " --> pdb=" O ARG A1442 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A1447 " --> pdb=" O LEU A1444 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A1451 " --> pdb=" O ALA A1448 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE A1454 " --> pdb=" O VAL A1451 " (cutoff:3.500A) Processing helix chain 'A' and resid 1470 through 1474 removed outlier: 3.757A pdb=" N ARG A1474 " --> pdb=" O PRO A1470 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1470 through 1474' Processing helix chain 'A' and resid 1493 through 1503 removed outlier: 4.952A pdb=" N PHE A1502 " --> pdb=" O GLU A1498 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A1503 " --> pdb=" O LEU A1499 " (cutoff:3.500A) Processing helix chain 'A' and resid 1515 through 1518 No H-bonds generated for 'chain 'A' and resid 1515 through 1518' Processing helix chain 'A' and resid 1531 through 1584 removed outlier: 4.748A pdb=" N ILE A1550 " --> pdb=" O VAL A1546 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN A1551 " --> pdb=" O VAL A1547 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG A1563 " --> pdb=" O ASP A1559 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA A1566 " --> pdb=" O GLN A1562 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN A1567 " --> pdb=" O ARG A1563 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A1570 " --> pdb=" O ALA A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1596 through 1599 No H-bonds generated for 'chain 'A' and resid 1596 through 1599' Processing helix chain 'A' and resid 1671 through 1673 No H-bonds generated for 'chain 'A' and resid 1671 through 1673' Processing helix chain 'A' and resid 1677 through 1688 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 179 through 187 Proline residue: B 187 - end of helix Processing helix chain 'B' and resid 201 through 207 Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 236 through 242 Processing helix chain 'B' and resid 252 through 260 Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 304 through 311 Processing helix chain 'B' and resid 314 through 322 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 348 through 355 Processing helix chain 'B' and resid 372 through 378 Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.799A pdb=" N MET B 386 " --> pdb=" O GLU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 411 Processing helix chain 'B' and resid 414 through 423 Processing helix chain 'B' and resid 438 through 444 removed outlier: 4.571A pdb=" N GLU B 443 " --> pdb=" O HIS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 471 through 475 Processing helix chain 'B' and resid 481 through 490 removed outlier: 4.320A pdb=" N ALA B 485 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU B 486 " --> pdb=" O ARG B 483 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS B 490 " --> pdb=" O MET B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 512 Processing helix chain 'B' and resid 515 through 523 Processing helix chain 'B' and resid 538 through 544 Processing helix chain 'B' and resid 548 through 561 removed outlier: 3.730A pdb=" N GLU B 560 " --> pdb=" O GLU B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 571 Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 581 through 586 removed outlier: 3.737A pdb=" N CYS B 586 " --> pdb=" O LEU B 582 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'B' and resid 624 through 631 removed outlier: 3.682A pdb=" N CYS B 628 " --> pdb=" O ALA B 624 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 629 " --> pdb=" O PHE B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 637 through 643 Processing helix chain 'B' and resid 648 through 653 Processing helix chain 'B' and resid 663 through 670 Processing helix chain 'B' and resid 673 through 681 Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 706 through 714 Processing helix chain 'B' and resid 729 through 736 Processing helix chain 'B' and resid 739 through 749 Processing helix chain 'B' and resid 763 through 770 removed outlier: 3.818A pdb=" N SER B 770 " --> pdb=" O LEU B 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 782 Processing helix chain 'B' and resid 796 through 802 Processing helix chain 'B' and resid 806 through 814 Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'B' and resid 830 through 837 Processing helix chain 'B' and resid 840 through 855 removed outlier: 8.169A pdb=" N SER B 852 " --> pdb=" O LYS B 848 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY B 853 " --> pdb=" O PHE B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 873 Processing helix chain 'B' and resid 876 through 885 Processing helix chain 'B' and resid 899 through 906 Processing helix chain 'B' and resid 909 through 918 removed outlier: 4.022A pdb=" N THR B 918 " --> pdb=" O VAL B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 932 through 938 Processing helix chain 'B' and resid 942 through 951 Processing helix chain 'B' and resid 978 through 985 Processing helix chain 'B' and resid 988 through 996 removed outlier: 3.644A pdb=" N ASN B 996 " --> pdb=" O ARG B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1018 Processing helix chain 'B' and resid 1023 through 1032 Processing helix chain 'B' and resid 1047 through 1054 Processing helix chain 'B' and resid 1057 through 1066 Processing helix chain 'B' and resid 1080 through 1087 Processing helix chain 'B' and resid 1090 through 1098 Processing helix chain 'B' and resid 1113 through 1119 Processing helix chain 'B' and resid 1123 through 1131 Processing helix chain 'B' and resid 1136 through 1139 No H-bonds generated for 'chain 'B' and resid 1136 through 1139' Processing helix chain 'B' and resid 1143 through 1155 Processing helix chain 'B' and resid 1159 through 1167 Processing helix chain 'B' and resid 1171 through 1188 removed outlier: 3.652A pdb=" N THR B1187 " --> pdb=" O ILE B1183 " (cutoff:3.500A) Processing helix chain 'B' and resid 1193 through 1215 removed outlier: 3.839A pdb=" N VAL B1197 " --> pdb=" O ALA B1193 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B1198 " --> pdb=" O LYS B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1220 through 1224 Processing helix chain 'B' and resid 1234 through 1240 Processing helix chain 'B' and resid 1244 through 1247 No H-bonds generated for 'chain 'B' and resid 1244 through 1247' Processing helix chain 'B' and resid 1250 through 1261 Processing helix chain 'B' and resid 1270 through 1280 removed outlier: 3.917A pdb=" N VAL B1276 " --> pdb=" O LEU B1272 " (cutoff:3.500A) Processing helix chain 'B' and resid 1282 through 1289 Processing helix chain 'B' and resid 1300 through 1322 Processing helix chain 'B' and resid 1338 through 1356 Processing helix chain 'B' and resid 1363 through 1386 removed outlier: 4.073A pdb=" N ILE B1367 " --> pdb=" O LEU B1364 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY B1375 " --> pdb=" O LEU B1372 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N MET B1376 " --> pdb=" O LEU B1373 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL B1379 " --> pdb=" O MET B1376 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL B1383 " --> pdb=" O GLY B1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 1396 through 1418 Processing helix chain 'B' and resid 1428 through 1461 removed outlier: 3.952A pdb=" N ILE B1433 " --> pdb=" O ALA B1430 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B1434 " --> pdb=" O ILE B1431 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP B1435 " --> pdb=" O ILE B1432 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP B1439 " --> pdb=" O LEU B1436 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B1440 " --> pdb=" O LEU B1437 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA B1445 " --> pdb=" O ARG B1442 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B1447 " --> pdb=" O LEU B1444 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B1451 " --> pdb=" O ALA B1448 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B1454 " --> pdb=" O VAL B1451 " (cutoff:3.500A) Processing helix chain 'B' and resid 1470 through 1474 removed outlier: 3.757A pdb=" N ARG B1474 " --> pdb=" O PRO B1470 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1470 through 1474' Processing helix chain 'B' and resid 1493 through 1503 removed outlier: 4.951A pdb=" N PHE B1502 " --> pdb=" O GLU B1498 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA B1503 " --> pdb=" O LEU B1499 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1518 No H-bonds generated for 'chain 'B' and resid 1515 through 1518' Processing helix chain 'B' and resid 1531 through 1584 removed outlier: 4.747A pdb=" N ILE B1550 " --> pdb=" O VAL B1546 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLN B1551 " --> pdb=" O VAL B1547 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ARG B1563 " --> pdb=" O ASP B1559 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ALA B1566 " --> pdb=" O GLN B1562 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN B1567 " --> pdb=" O ARG B1563 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE B1570 " --> pdb=" O ALA B1566 " (cutoff:3.500A) Processing helix chain 'B' and resid 1596 through 1599 No H-bonds generated for 'chain 'B' and resid 1596 through 1599' Processing helix chain 'B' and resid 1671 through 1673 No H-bonds generated for 'chain 'B' and resid 1671 through 1673' Processing helix chain 'B' and resid 1677 through 1688 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 145 through 156 Processing helix chain 'C' and resid 168 through 172 Processing helix chain 'C' and resid 179 through 187 Proline residue: C 187 - end of helix Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 236 through 242 Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 282 through 289 Processing helix chain 'C' and resid 304 through 311 Processing helix chain 'C' and resid 314 through 322 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 348 through 355 Processing helix chain 'C' and resid 372 through 378 Processing helix chain 'C' and resid 381 through 389 removed outlier: 3.800A pdb=" N MET C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 Processing helix chain 'C' and resid 414 through 423 Processing helix chain 'C' and resid 438 through 444 removed outlier: 4.571A pdb=" N GLU C 443 " --> pdb=" O HIS C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 456 Processing helix chain 'C' and resid 471 through 475 Processing helix chain 'C' and resid 481 through 490 removed outlier: 4.320A pdb=" N ALA C 485 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU C 486 " --> pdb=" O ARG C 483 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS C 490 " --> pdb=" O MET C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 505 through 512 Processing helix chain 'C' and resid 515 through 523 Processing helix chain 'C' and resid 538 through 544 Processing helix chain 'C' and resid 548 through 561 removed outlier: 3.729A pdb=" N GLU C 560 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 571 Processing helix chain 'C' and resid 576 through 578 No H-bonds generated for 'chain 'C' and resid 576 through 578' Processing helix chain 'C' and resid 581 through 586 removed outlier: 3.735A pdb=" N CYS C 586 " --> pdb=" O LEU C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 608 Processing helix chain 'C' and resid 624 through 631 removed outlier: 3.682A pdb=" N CYS C 628 " --> pdb=" O ALA C 624 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 629 " --> pdb=" O PHE C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 635 No H-bonds generated for 'chain 'C' and resid 633 through 635' Processing helix chain 'C' and resid 637 through 643 Processing helix chain 'C' and resid 648 through 653 Processing helix chain 'C' and resid 663 through 670 Processing helix chain 'C' and resid 673 through 681 Processing helix chain 'C' and resid 696 through 703 Processing helix chain 'C' and resid 706 through 714 Processing helix chain 'C' and resid 729 through 736 Processing helix chain 'C' and resid 739 through 749 Processing helix chain 'C' and resid 763 through 770 removed outlier: 3.818A pdb=" N SER C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 782 Processing helix chain 'C' and resid 796 through 802 Processing helix chain 'C' and resid 806 through 814 Processing helix chain 'C' and resid 820 through 822 No H-bonds generated for 'chain 'C' and resid 820 through 822' Processing helix chain 'C' and resid 830 through 837 Processing helix chain 'C' and resid 840 through 855 removed outlier: 8.170A pdb=" N SER C 852 " --> pdb=" O LYS C 848 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY C 853 " --> pdb=" O PHE C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 873 Processing helix chain 'C' and resid 876 through 885 Processing helix chain 'C' and resid 899 through 906 Processing helix chain 'C' and resid 909 through 918 removed outlier: 4.022A pdb=" N THR C 918 " --> pdb=" O VAL C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 938 Processing helix chain 'C' and resid 942 through 951 Processing helix chain 'C' and resid 978 through 985 Processing helix chain 'C' and resid 988 through 996 removed outlier: 3.643A pdb=" N ASN C 996 " --> pdb=" O ARG C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1018 Processing helix chain 'C' and resid 1023 through 1032 Processing helix chain 'C' and resid 1047 through 1054 Processing helix chain 'C' and resid 1057 through 1066 Processing helix chain 'C' and resid 1080 through 1087 Processing helix chain 'C' and resid 1090 through 1098 Processing helix chain 'C' and resid 1113 through 1119 Processing helix chain 'C' and resid 1123 through 1131 Processing helix chain 'C' and resid 1136 through 1139 No H-bonds generated for 'chain 'C' and resid 1136 through 1139' Processing helix chain 'C' and resid 1143 through 1155 Processing helix chain 'C' and resid 1159 through 1167 Processing helix chain 'C' and resid 1171 through 1188 removed outlier: 3.652A pdb=" N THR C1187 " --> pdb=" O ILE C1183 " (cutoff:3.500A) Processing helix chain 'C' and resid 1193 through 1215 removed outlier: 3.839A pdb=" N VAL C1197 " --> pdb=" O ALA C1193 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA C1198 " --> pdb=" O LYS C1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1224 Processing helix chain 'C' and resid 1234 through 1240 Processing helix chain 'C' and resid 1244 through 1247 No H-bonds generated for 'chain 'C' and resid 1244 through 1247' Processing helix chain 'C' and resid 1250 through 1261 Processing helix chain 'C' and resid 1270 through 1280 removed outlier: 3.918A pdb=" N VAL C1276 " --> pdb=" O LEU C1272 " (cutoff:3.500A) Processing helix chain 'C' and resid 1282 through 1289 Processing helix chain 'C' and resid 1300 through 1322 Processing helix chain 'C' and resid 1338 through 1356 Processing helix chain 'C' and resid 1363 through 1386 removed outlier: 4.073A pdb=" N ILE C1367 " --> pdb=" O LEU C1364 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C1375 " --> pdb=" O LEU C1372 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET C1376 " --> pdb=" O LEU C1373 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL C1379 " --> pdb=" O MET C1376 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL C1383 " --> pdb=" O GLY C1380 " (cutoff:3.500A) Processing helix chain 'C' and resid 1396 through 1418 Processing helix chain 'C' and resid 1428 through 1461 removed outlier: 3.951A pdb=" N ILE C1433 " --> pdb=" O ALA C1430 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C1434 " --> pdb=" O ILE C1431 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP C1435 " --> pdb=" O ILE C1432 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP C1439 " --> pdb=" O LEU C1436 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU C1440 " --> pdb=" O LEU C1437 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA C1445 " --> pdb=" O ARG C1442 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C1447 " --> pdb=" O LEU C1444 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C1451 " --> pdb=" O ALA C1448 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE C1454 " --> pdb=" O VAL C1451 " (cutoff:3.500A) Processing helix chain 'C' and resid 1470 through 1474 removed outlier: 3.757A pdb=" N ARG C1474 " --> pdb=" O PRO C1470 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1470 through 1474' Processing helix chain 'C' and resid 1493 through 1503 removed outlier: 4.951A pdb=" N PHE C1502 " --> pdb=" O GLU C1498 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA C1503 " --> pdb=" O LEU C1499 " (cutoff:3.500A) Processing helix chain 'C' and resid 1515 through 1518 No H-bonds generated for 'chain 'C' and resid 1515 through 1518' Processing helix chain 'C' and resid 1531 through 1584 removed outlier: 4.748A pdb=" N ILE C1550 " --> pdb=" O VAL C1546 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN C1551 " --> pdb=" O VAL C1547 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARG C1563 " --> pdb=" O ASP C1559 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA C1566 " --> pdb=" O GLN C1562 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN C1567 " --> pdb=" O ARG C1563 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C1570 " --> pdb=" O ALA C1566 " (cutoff:3.500A) Processing helix chain 'C' and resid 1596 through 1599 No H-bonds generated for 'chain 'C' and resid 1596 through 1599' Processing helix chain 'C' and resid 1671 through 1673 No H-bonds generated for 'chain 'C' and resid 1671 through 1673' Processing helix chain 'C' and resid 1677 through 1688 Processing helix chain 'D' and resid 133 through 138 Processing helix chain 'D' and resid 145 through 156 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 179 through 187 Proline residue: D 187 - end of helix Processing helix chain 'D' and resid 201 through 207 Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 236 through 242 Processing helix chain 'D' and resid 252 through 260 Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 282 through 289 Processing helix chain 'D' and resid 304 through 311 Processing helix chain 'D' and resid 314 through 322 Processing helix chain 'D' and resid 337 through 344 Processing helix chain 'D' and resid 348 through 355 Processing helix chain 'D' and resid 372 through 378 Processing helix chain 'D' and resid 381 through 389 removed outlier: 3.800A pdb=" N MET D 386 " --> pdb=" O GLU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 414 through 423 Processing helix chain 'D' and resid 438 through 444 removed outlier: 4.571A pdb=" N GLU D 443 " --> pdb=" O HIS D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 456 Processing helix chain 'D' and resid 471 through 475 Processing helix chain 'D' and resid 481 through 490 removed outlier: 4.320A pdb=" N ALA D 485 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LEU D 486 " --> pdb=" O ARG D 483 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS D 490 " --> pdb=" O MET D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 512 Processing helix chain 'D' and resid 515 through 523 Processing helix chain 'D' and resid 538 through 544 Processing helix chain 'D' and resid 548 through 561 removed outlier: 3.729A pdb=" N GLU D 560 " --> pdb=" O GLU D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 571 Processing helix chain 'D' and resid 576 through 578 No H-bonds generated for 'chain 'D' and resid 576 through 578' Processing helix chain 'D' and resid 581 through 586 removed outlier: 3.736A pdb=" N CYS D 586 " --> pdb=" O LEU D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 608 Processing helix chain 'D' and resid 624 through 631 removed outlier: 3.682A pdb=" N CYS D 628 " --> pdb=" O ALA D 624 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 629 " --> pdb=" O PHE D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 635 No H-bonds generated for 'chain 'D' and resid 633 through 635' Processing helix chain 'D' and resid 637 through 643 Processing helix chain 'D' and resid 648 through 653 Processing helix chain 'D' and resid 663 through 670 Processing helix chain 'D' and resid 673 through 681 Processing helix chain 'D' and resid 696 through 703 Processing helix chain 'D' and resid 706 through 714 Processing helix chain 'D' and resid 729 through 736 Processing helix chain 'D' and resid 739 through 749 Processing helix chain 'D' and resid 763 through 770 removed outlier: 3.818A pdb=" N SER D 770 " --> pdb=" O LEU D 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 773 through 782 Processing helix chain 'D' and resid 796 through 802 Processing helix chain 'D' and resid 806 through 814 Processing helix chain 'D' and resid 820 through 822 No H-bonds generated for 'chain 'D' and resid 820 through 822' Processing helix chain 'D' and resid 830 through 837 Processing helix chain 'D' and resid 840 through 855 removed outlier: 8.169A pdb=" N SER D 852 " --> pdb=" O LYS D 848 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY D 853 " --> pdb=" O PHE D 849 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 873 Processing helix chain 'D' and resid 876 through 885 Processing helix chain 'D' and resid 899 through 906 Processing helix chain 'D' and resid 909 through 918 removed outlier: 4.022A pdb=" N THR D 918 " --> pdb=" O VAL D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 932 through 938 Processing helix chain 'D' and resid 942 through 951 Processing helix chain 'D' and resid 978 through 985 Processing helix chain 'D' and resid 988 through 996 removed outlier: 3.644A pdb=" N ASN D 996 " --> pdb=" O ARG D 992 " (cutoff:3.500A) Processing helix chain 'D' and resid 1013 through 1018 Processing helix chain 'D' and resid 1023 through 1032 Processing helix chain 'D' and resid 1047 through 1054 Processing helix chain 'D' and resid 1057 through 1066 Processing helix chain 'D' and resid 1080 through 1087 Processing helix chain 'D' and resid 1090 through 1098 Processing helix chain 'D' and resid 1113 through 1119 Processing helix chain 'D' and resid 1123 through 1131 Processing helix chain 'D' and resid 1136 through 1139 No H-bonds generated for 'chain 'D' and resid 1136 through 1139' Processing helix chain 'D' and resid 1143 through 1155 Processing helix chain 'D' and resid 1159 through 1167 Processing helix chain 'D' and resid 1171 through 1188 removed outlier: 3.653A pdb=" N THR D1187 " --> pdb=" O ILE D1183 " (cutoff:3.500A) Processing helix chain 'D' and resid 1193 through 1215 removed outlier: 3.839A pdb=" N VAL D1197 " --> pdb=" O ALA D1193 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA D1198 " --> pdb=" O LYS D1194 " (cutoff:3.500A) Processing helix chain 'D' and resid 1220 through 1224 Processing helix chain 'D' and resid 1234 through 1240 Processing helix chain 'D' and resid 1244 through 1247 No H-bonds generated for 'chain 'D' and resid 1244 through 1247' Processing helix chain 'D' and resid 1250 through 1261 Processing helix chain 'D' and resid 1270 through 1280 removed outlier: 3.918A pdb=" N VAL D1276 " --> pdb=" O LEU D1272 " (cutoff:3.500A) Processing helix chain 'D' and resid 1282 through 1289 Processing helix chain 'D' and resid 1300 through 1322 Processing helix chain 'D' and resid 1338 through 1356 Processing helix chain 'D' and resid 1363 through 1386 removed outlier: 4.072A pdb=" N ILE D1367 " --> pdb=" O LEU D1364 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY D1375 " --> pdb=" O LEU D1372 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N MET D1376 " --> pdb=" O LEU D1373 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL D1379 " --> pdb=" O MET D1376 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL D1383 " --> pdb=" O GLY D1380 " (cutoff:3.500A) Processing helix chain 'D' and resid 1396 through 1418 Processing helix chain 'D' and resid 1428 through 1461 removed outlier: 3.951A pdb=" N ILE D1433 " --> pdb=" O ALA D1430 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLY D1434 " --> pdb=" O ILE D1431 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP D1435 " --> pdb=" O ILE D1432 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP D1439 " --> pdb=" O LEU D1436 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D1440 " --> pdb=" O LEU D1437 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA D1445 " --> pdb=" O ARG D1442 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D1447 " --> pdb=" O LEU D1444 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL D1451 " --> pdb=" O ALA D1448 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE D1454 " --> pdb=" O VAL D1451 " (cutoff:3.500A) Processing helix chain 'D' and resid 1470 through 1474 removed outlier: 3.756A pdb=" N ARG D1474 " --> pdb=" O PRO D1470 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1470 through 1474' Processing helix chain 'D' and resid 1493 through 1503 removed outlier: 4.952A pdb=" N PHE D1502 " --> pdb=" O GLU D1498 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA D1503 " --> pdb=" O LEU D1499 " (cutoff:3.500A) Processing helix chain 'D' and resid 1515 through 1518 No H-bonds generated for 'chain 'D' and resid 1515 through 1518' Processing helix chain 'D' and resid 1531 through 1584 removed outlier: 4.748A pdb=" N ILE D1550 " --> pdb=" O VAL D1546 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN D1551 " --> pdb=" O VAL D1547 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ARG D1563 " --> pdb=" O ASP D1559 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ALA D1566 " --> pdb=" O GLN D1562 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN D1567 " --> pdb=" O ARG D1563 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE D1570 " --> pdb=" O ALA D1566 " (cutoff:3.500A) Processing helix chain 'D' and resid 1596 through 1599 No H-bonds generated for 'chain 'D' and resid 1596 through 1599' Processing helix chain 'D' and resid 1671 through 1673 No H-bonds generated for 'chain 'D' and resid 1671 through 1673' Processing helix chain 'D' and resid 1677 through 1688 1880 hydrogen bonds defined for protein. 5136 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: 15.92 Time building geometry restraints manager: 17.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7784 1.33 - 1.45: 9955 1.45 - 1.57: 24509 1.57 - 1.69: 100 1.69 - 1.82: 304 Bond restraints: 42652 Sorted by residual: bond pdb=" O14 PCF C1804 " pdb=" P PCF C1804 " ideal model delta sigma weight residual 1.510 1.619 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" O14 PCF C1801 " pdb=" P PCF C1801 " ideal model delta sigma weight residual 1.510 1.619 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" O14 PCF A1807 " pdb=" P PCF A1807 " ideal model delta sigma weight residual 1.510 1.619 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" O14 PCF D1808 " pdb=" P PCF D1808 " ideal model delta sigma weight residual 1.510 1.618 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" O14 PCF A1803 " pdb=" P PCF A1803 " ideal model delta sigma weight residual 1.510 1.618 -0.108 2.00e-02 2.50e+03 2.94e+01 ... (remaining 42647 not shown) Histogram of bond angle deviations from ideal: 97.83 - 105.08: 698 105.08 - 112.33: 23221 112.33 - 119.59: 13033 119.59 - 126.84: 20696 126.84 - 134.10: 636 Bond angle restraints: 58284 Sorted by residual: angle pdb=" N ASN A 924 " pdb=" CA ASN A 924 " pdb=" C ASN A 924 " ideal model delta sigma weight residual 110.24 119.99 -9.75 1.47e+00 4.63e-01 4.40e+01 angle pdb=" N ASN C 924 " pdb=" CA ASN C 924 " pdb=" C ASN C 924 " ideal model delta sigma weight residual 110.24 119.99 -9.75 1.47e+00 4.63e-01 4.40e+01 angle pdb=" N ASN B 924 " pdb=" CA ASN B 924 " pdb=" C ASN B 924 " ideal model delta sigma weight residual 110.24 119.99 -9.75 1.47e+00 4.63e-01 4.40e+01 angle pdb=" N ASN D 924 " pdb=" CA ASN D 924 " pdb=" C ASN D 924 " ideal model delta sigma weight residual 110.24 119.97 -9.73 1.47e+00 4.63e-01 4.38e+01 angle pdb=" C ASN C 803 " pdb=" N ASN C 804 " pdb=" CA ASN C 804 " ideal model delta sigma weight residual 122.46 130.70 -8.24 1.41e+00 5.03e-01 3.42e+01 ... (remaining 58279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.08: 24159 25.08 - 50.15: 657 50.15 - 75.23: 68 75.23 - 100.31: 0 100.31 - 125.39: 4 Dihedral angle restraints: 24888 sinusoidal: 7592 harmonic: 17296 Sorted by residual: dihedral pdb=" CA HIS A 461 " pdb=" C HIS A 461 " pdb=" N VAL A 462 " pdb=" CA VAL A 462 " ideal model delta harmonic sigma weight residual -180.00 -131.35 -48.65 0 5.00e+00 4.00e-02 9.47e+01 dihedral pdb=" CA HIS B 461 " pdb=" C HIS B 461 " pdb=" N VAL B 462 " pdb=" CA VAL B 462 " ideal model delta harmonic sigma weight residual -180.00 -131.37 -48.63 0 5.00e+00 4.00e-02 9.46e+01 dihedral pdb=" CA HIS D 461 " pdb=" C HIS D 461 " pdb=" N VAL D 462 " pdb=" CA VAL D 462 " ideal model delta harmonic sigma weight residual -180.00 -131.39 -48.61 0 5.00e+00 4.00e-02 9.45e+01 ... (remaining 24885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 5512 0.057 - 0.114: 1353 0.114 - 0.172: 196 0.172 - 0.229: 35 0.229 - 0.286: 20 Chirality restraints: 7116 Sorted by residual: chirality pdb=" CB ILE D1564 " pdb=" CA ILE D1564 " pdb=" CG1 ILE D1564 " pdb=" CG2 ILE D1564 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CB ILE C1564 " pdb=" CA ILE C1564 " pdb=" CG1 ILE C1564 " pdb=" CG2 ILE C1564 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE A1564 " pdb=" CA ILE A1564 " pdb=" CG1 ILE A1564 " pdb=" CG2 ILE A1564 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 7113 not shown) Planarity restraints: 7384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B1591 " -0.065 5.00e-02 4.00e+02 9.92e-02 1.57e+01 pdb=" N PRO B1592 " 0.172 5.00e-02 4.00e+02 pdb=" CA PRO B1592 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B1592 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D1591 " 0.065 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO D1592 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO D1592 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D1592 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C1591 " -0.065 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO C1592 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO C1592 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C1592 " -0.056 5.00e-02 4.00e+02 ... (remaining 7381 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 448 2.63 - 3.19: 37793 3.19 - 3.76: 65603 3.76 - 4.33: 90354 4.33 - 4.90: 141247 Nonbonded interactions: 335445 Sorted by model distance: nonbonded pdb=" OH TYR C1532 " pdb=" O11 PCF C1801 " model vdw 2.057 2.440 nonbonded pdb=" OH TYR A1532 " pdb=" O11 PCF A1803 " model vdw 2.059 2.440 nonbonded pdb=" CE2 TYR C1532 " pdb=" C22 PCF C1801 " model vdw 2.097 3.740 nonbonded pdb=" CB GLU C1498 " pdb=" C35 PCF D1801 " model vdw 2.200 3.840 nonbonded pdb=" CB GLU A1498 " pdb=" C35 PCF B1808 " model vdw 2.206 3.840 ... (remaining 335440 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' and (resid 124 through 1689 or (resid 1801 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or resid 1 \ 802 or (resid 1803 through 1804 and (name C1 or name C2 or name C21 or name C3 o \ r name C31 or name C32 or name C33 or name C34 or name C35 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or na \ me P )) or (resid 1805 and (name C1 or name C2 or name C21 or name C22 or name C \ 23 or name C24 or name C25 or name C3 or name C31 or name C32 or name C33 or nam \ e C34 or name C35 or name C36 or name C37 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or resid \ 1806 or (resid 1807 and (name C1 or name C2 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name \ C3 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or na \ me C37 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 o \ r name O31 or name O32 or name P )) or (resid 1808 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C3 or name C31 or \ name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name O1 \ 1 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or nam \ e O32 or name P )))) selection = (chain 'B' and (resid 124 through 1689 or (resid 1801 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (resid \ 1802 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or n \ ame O32 or name P )) or (resid 1803 through 1804 and (name C1 or name C2 or name \ C21 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 \ or name O32 or name P )) or (resid 1805 and (name C1 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or na \ me P )) or (resid 1806 and (name C1 or name C2 or name C21 or name C3 or name C3 \ 1 or name C32 or name C33 or name C34 or name C35 or name O11 or name O12 or nam \ e O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) o \ r resid 1807 or (resid 1808 and (name C1 or name C2 or name C21 or name C22 or n \ ame C23 or name C24 or name C25 or name C3 or name C31 or name C32 or name C33 o \ r name C34 or name C35 or name C36 or name C37 or name O11 or name O12 or name O \ 13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )))) selection = (chain 'C' and (resid 124 through 1689 or (resid 1801 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (resid \ 1802 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or n \ ame O32 or name P )) or (resid 1803 through 1804 and (name C1 or name C2 or name \ C21 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 \ or name O32 or name P )) or (resid 1805 and (name C1 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or na \ me P )) or (resid 1806 and (name C1 or name C2 or name C21 or name C3 or name C3 \ 1 or name C32 or name C33 or name C34 or name C35 or name O11 or name O12 or nam \ e O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) o \ r (resid 1807 and (name C1 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ O31 or name O32 or name P )) or (resid 1808 and (name C1 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or n \ ame O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 \ or name P )))) selection = (chain 'D' and (resid 124 through 1689 or (resid 1801 and (name C1 or name C2 or \ name C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C2 \ 7 or name C28 or name C3 or name C31 or name C32 or name C33 or name C34 or name \ C35 or name C36 or name C37 or name C38 or name O11 or name O12 or name O13 or \ name O14 or name O21 or name O22 or name O31 or name O32 or name P )) or (resid \ 1802 and (name C1 or name C2 or name C21 or name C22 or name C23 or name C24 or \ name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or name C31 \ or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name \ O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or n \ ame O32 or name P )) or (resid 1803 through 1804 and (name C1 or name C2 or name \ C21 or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 \ or name O32 or name P )) or (resid 1805 and (name C1 or name C2 or name C21 or n \ ame C22 or name C23 or name C24 or name C25 or name C3 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or name O \ 12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or na \ me P )) or (resid 1806 and (name C1 or name C2 or name C21 or name C3 or name C3 \ 1 or name C32 or name C33 or name C34 or name C35 or name O11 or name O12 or nam \ e O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P )) o \ r (resid 1807 and (name C1 or name C2 or name C21 or name C22 or name C23 or nam \ e C24 or name C25 or name C26 or name C27 or name C28 or name C29 or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ O31 or name O32 or name P )) or (resid 1808 and (name C1 or name C2 or name C21 \ or name C22 or name C23 or name C24 or name C25 or name C3 or name C31 or name \ C32 or name C33 or name C34 or name C35 or name C36 or name C37 or name O11 or n \ ame O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name O32 \ or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 11.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 14.550 Check model and map are aligned: 0.620 Set scattering table: 0.350 Process input model: 105.810 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.008 0.109 42652 Z= 0.501 Angle : 1.182 11.564 58284 Z= 0.652 Chirality : 0.052 0.286 7116 Planarity : 0.007 0.099 7384 Dihedral : 11.887 125.386 13704 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 8.90 % Favored : 90.77 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.41 % 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: -5.28 (0.08), residues: 5980 helix: -3.43 (0.05), residues: 3608 sheet: None (None), residues: 0 loop : -3.41 (0.10), residues: 2372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 763 time to evaluate : 4.412 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 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 783 average time/residue: 0.5266 time to fit residues: 692.9762 Evaluate side-chains 403 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 395 time to evaluate : 4.557 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3717 time to fit residues: 11.7431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 503 optimal weight: 7.9990 chunk 451 optimal weight: 50.0000 chunk 250 optimal weight: 2.9990 chunk 154 optimal weight: 50.0000 chunk 304 optimal weight: 50.0000 chunk 241 optimal weight: 3.9990 chunk 467 optimal weight: 0.0060 chunk 180 optimal weight: 3.9990 chunk 284 optimal weight: 6.9990 chunk 347 optimal weight: 5.9990 chunk 541 optimal weight: 4.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 583 HIS A 643 HIS A 654 ASN A 669 HIS A 682 ASN A 707 HIS A 798 HIS A 832 HIS ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 HIS A1038 GLN A1056 HIS A1108 ASN A1134 HIS A1249 HIS A1297 ASN B 583 HIS B 616 GLN B 643 HIS B 654 ASN B 669 HIS B 798 HIS B 832 HIS ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 HIS B1038 GLN B1056 HIS B1108 ASN B1249 HIS B1297 ASN ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 HIS ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 HIS C 654 ASN C 669 HIS C 682 ASN C 798 HIS C 832 HIS ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1022 HIS C1038 GLN C1056 HIS C1108 ASN C1249 HIS C1297 ASN C1311 HIS ** C1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 547 HIS ** D 583 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 643 HIS D 654 ASN D 682 ASN D 798 HIS D 832 HIS ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1022 HIS D1038 GLN D1056 HIS D1108 ASN D1249 HIS D1297 ASN ** D1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.077 42652 Z= 0.533 Angle : 0.867 11.489 58284 Z= 0.448 Chirality : 0.046 0.183 7116 Planarity : 0.006 0.084 7384 Dihedral : 10.619 88.526 6820 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.22 % Favored : 89.60 % Rotamer Outliers : 3.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.36 % 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: -3.29 (0.09), residues: 5980 helix: -1.54 (0.07), residues: 3772 sheet: None (None), residues: 0 loop : -3.22 (0.11), residues: 2208 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 419 time to evaluate : 4.637 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: 129 outliers final: 58 residues processed: 530 average time/residue: 0.5042 time to fit residues: 460.2148 Evaluate side-chains 405 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 347 time to evaluate : 4.535 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.4198 time to fit residues: 50.0450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 300 optimal weight: 30.0000 chunk 167 optimal weight: 20.0000 chunk 450 optimal weight: 0.9980 chunk 368 optimal weight: 0.8980 chunk 149 optimal weight: 80.0000 chunk 542 optimal weight: 0.5980 chunk 585 optimal weight: 0.0470 chunk 482 optimal weight: 7.9990 chunk 537 optimal weight: 0.6980 chunk 184 optimal weight: 9.9990 chunk 434 optimal weight: 0.4980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 601 GLN A 736 ASN ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 GLN A1257 GLN ** A1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1423 HIS ** A1457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN B 736 ASN ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 GLN B1482 ASN C 553 HIS C 601 GLN C 616 GLN C 736 ASN ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1162 GLN ** C1382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1423 HIS ** C1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 601 GLN D 736 ASN ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1162 GLN ** D1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1423 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 42652 Z= 0.178 Angle : 0.637 10.143 58284 Z= 0.325 Chirality : 0.039 0.168 7116 Planarity : 0.004 0.071 7384 Dihedral : 9.504 90.851 6820 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.79 % Favored : 92.12 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.12 % 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: -2.25 (0.10), residues: 5980 helix: -0.67 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : -2.88 (0.12), residues: 2260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11960 Ramachandran restraints generated. 5980 Oldfield, 0 Emsley, 5980 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 448 time to evaluate : 4.908 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 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: 75 outliers final: 23 residues processed: 509 average time/residue: 0.4737 time to fit residues: 418.7389 Evaluate side-chains 414 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 391 time to evaluate : 4.536 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3707 time to fit residues: 22.0099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.217 > 50: distance: 5 - 19: 7.729 distance: 9 - 24: 21.010 distance: 13 - 28: 27.415 distance: 16 - 19: 5.489 distance: 17 - 33: 24.058 distance: 19 - 20: 8.831 distance: 20 - 21: 25.351 distance: 20 - 23: 6.487 distance: 21 - 22: 18.217 distance: 21 - 24: 18.815 distance: 24 - 25: 15.231 distance: 25 - 26: 11.523 distance: 26 - 27: 17.255 distance: 26 - 28: 7.202 distance: 28 - 29: 26.182 distance: 29 - 30: 45.760 distance: 29 - 32: 42.150 distance: 30 - 31: 56.169 distance: 30 - 33: 27.583 distance: 33 - 34: 26.281 distance: 34 - 35: 23.970 distance: 34 - 37: 18.962 distance: 35 - 36: 35.495 distance: 35 - 38: 23.626 distance: 38 - 39: 19.739 distance: 39 - 40: 21.547 distance: 39 - 42: 25.200 distance: 40 - 41: 11.277 distance: 40 - 43: 18.264 distance: 43 - 44: 22.195 distance: 44 - 45: 29.496 distance: 44 - 47: 16.603 distance: 45 - 46: 27.996 distance: 45 - 48: 39.140 distance: 48 - 49: 13.575 distance: 49 - 50: 51.623 distance: 49 - 52: 20.942 distance: 50 - 51: 45.082 distance: 50 - 53: 44.865 distance: 53 - 54: 24.554 distance: 54 - 55: 34.107 distance: 54 - 57: 25.757 distance: 55 - 56: 33.504 distance: 55 - 58: 18.743 distance: 58 - 59: 14.285 distance: 59 - 60: 33.922 distance: 60 - 61: 44.143 distance: 60 - 62: 32.067 distance: 62 - 63: 28.197 distance: 63 - 64: 48.613 distance: 64 - 65: 45.051 distance: 64 - 66: 24.836