Starting phenix.real_space_refine on Sat Feb 24 06:41:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/02_2024/5vkq_8702_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/02_2024/5vkq_8702.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/02_2024/5vkq_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_8702/02_2024/5vkq_8702_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/02_2024/5vkq_8702_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/02_2024/5vkq_8702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/02_2024/5vkq_8702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/02_2024/5vkq_8702_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5vkq_8702/02_2024/5vkq_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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 22.47, per 1000 atoms: 0.54 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: 17.59 Conformation dependent library (CDL) restraints added in 8.2 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: 13.84 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: 18.05 Time building geometry restraints manager: 18.90 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: 24187 25.08 - 50.15: 681 50.15 - 75.23: 80 75.23 - 100.31: 0 100.31 - 125.39: 4 Dihedral angle restraints: 24952 sinusoidal: 7656 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 24949 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: 3.430 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: 0.030 Extract box with map and model: 15.540 Check model and map are aligned: 0.760 Set scattering table: 0.450 Process input model: 115.940 Find NCS groups from input model: 3.270 Set up NCS constraints: 0.300 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: 0.020 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.710 ------------------------------------------------------------------------------- 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 : 12.105 125.386 13768 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 % Allowed : 4.19 % Favored : 95.10 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP D1429 HIS 0.018 0.003 HIS D 643 PHE 0.037 0.003 PHE B1505 TYR 0.035 0.003 TYR C1327 ARG 0.006 0.001 ARG B1331 *********************** 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 : 4.602 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 REVERT: A 386 MET cc_start: 0.8261 (mmm) cc_final: 0.7075 (ppp) REVERT: A 621 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9022 (tp) REVERT: A 1104 LYS cc_start: 0.8574 (mttt) cc_final: 0.7946 (mtmm) REVERT: A 1294 HIS cc_start: 0.5735 (t-90) cc_final: 0.5205 (t-90) REVERT: A 1348 SER cc_start: 0.8480 (t) cc_final: 0.8259 (p) REVERT: A 1399 TYR cc_start: 0.8864 (t80) cc_final: 0.8567 (t80) REVERT: A 1553 LEU cc_start: 0.9018 (tt) cc_final: 0.8785 (tt) REVERT: A 1592 PRO cc_start: 0.8145 (Cg_endo) cc_final: 0.7500 (Cg_exo) REVERT: B 386 MET cc_start: 0.8227 (mmm) cc_final: 0.7099 (ppp) REVERT: B 570 TYR cc_start: 0.8725 (t80) cc_final: 0.8419 (t80) REVERT: B 621 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9024 (tt) REVERT: B 1292 MET cc_start: 0.5213 (pp-130) cc_final: 0.3840 (tmm) REVERT: B 1312 ILE cc_start: 0.9291 (mt) cc_final: 0.9090 (mt) REVERT: B 1592 PRO cc_start: 0.8135 (Cg_endo) cc_final: 0.7639 (Cg_exo) REVERT: C 386 MET cc_start: 0.7964 (mmm) cc_final: 0.6901 (ppp) REVERT: C 387 LEU cc_start: 0.8951 (tp) cc_final: 0.8726 (tp) REVERT: C 621 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.9012 (tt) REVERT: C 943 ASP cc_start: 0.8042 (m-30) cc_final: 0.7793 (p0) REVERT: C 1104 LYS cc_start: 0.8623 (mttt) cc_final: 0.8019 (mtmm) REVERT: C 1292 MET cc_start: 0.4329 (pp-130) cc_final: 0.3552 (ttt) REVERT: C 1364 LEU cc_start: 0.8399 (mp) cc_final: 0.8185 (mt) REVERT: C 1368 LYS cc_start: 0.9087 (mttt) cc_final: 0.8798 (mtpp) REVERT: C 1456 MET cc_start: 0.7741 (mmm) cc_final: 0.7443 (mmt) REVERT: C 1592 PRO cc_start: 0.8125 (Cg_endo) cc_final: 0.7495 (Cg_exo) REVERT: D 386 MET cc_start: 0.8428 (mmm) cc_final: 0.7238 (ppp) REVERT: D 621 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8932 (tp) REVERT: D 1104 LYS cc_start: 0.8392 (mttt) cc_final: 0.8028 (mttp) REVERT: D 1292 MET cc_start: 0.4178 (pp-130) cc_final: 0.3385 (ttt) REVERT: D 1364 LEU cc_start: 0.8406 (mp) cc_final: 0.8178 (mt) REVERT: D 1368 LYS cc_start: 0.9119 (mttt) cc_final: 0.8914 (mtpp) REVERT: D 1376 MET cc_start: 0.7580 (mtt) cc_final: 0.7365 (mtp) REVERT: D 1592 PRO cc_start: 0.8171 (Cg_endo) cc_final: 0.7624 (Cg_exo) outliers start: 24 outliers final: 8 residues processed: 783 average time/residue: 0.5097 time to fit residues: 668.6214 Evaluate side-chains 415 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 403 time to evaluate : 5.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 1063 LEU Chi-restraints excluded: chain D residue 1235 LEU 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: 6.9990 chunk 541 optimal weight: 3.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS A 643 HIS A 654 ASN A 669 HIS A 707 HIS A 798 HIS A 832 HIS ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1038 GLN A1056 HIS A1108 ASN A1134 HIS A1249 HIS A1297 ASN A1423 HIS 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** B1038 GLN B1056 HIS B1108 ASN B1249 HIS B1297 ASN B1423 HIS ** C 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 HIS C 616 GLN C 643 HIS C 654 ASN C 669 HIS C 798 HIS C 832 HIS ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1022 HIS C1038 GLN C1056 HIS C1108 ASN C1134 HIS C1249 HIS C1297 ASN C1311 HIS C1423 HIS ** C1565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 547 HIS D 583 HIS D 643 HIS D 654 ASN D 669 HIS D 682 ASN D 798 HIS D 832 HIS ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1038 GLN D1056 HIS D1108 ASN D1249 HIS D1297 ASN D1423 HIS D1565 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 42652 Z= 0.498 Angle : 0.838 10.280 58284 Z= 0.433 Chirality : 0.045 0.202 7116 Planarity : 0.005 0.070 7384 Dihedral : 11.123 88.275 6908 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.98 % Favored : 89.83 % Rotamer: Outliers : 3.98 % Allowed : 10.65 % Favored : 85.38 % 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: -3.30 (0.09), residues: 5980 helix: -1.54 (0.07), residues: 3764 sheet: None (None), residues: 0 loop : -3.23 (0.11), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A1078 HIS 0.011 0.002 HIS A1294 PHE 0.022 0.002 PHE C1386 TYR 0.030 0.003 TYR A1339 ARG 0.006 0.001 ARG A1563 *********************** 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 559 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 426 time to evaluate : 5.144 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: A 386 MET cc_start: 0.8613 (mmm) cc_final: 0.7253 (tmm) REVERT: A 530 TYR cc_start: 0.7945 (OUTLIER) cc_final: 0.7555 (t80) REVERT: A 653 MET cc_start: 0.8247 (mtt) cc_final: 0.7825 (tmm) REVERT: A 1028 LEU cc_start: 0.9281 (mt) cc_final: 0.8965 (tp) REVERT: A 1173 ASP cc_start: 0.7611 (t0) cc_final: 0.6451 (t0) REVERT: A 1364 LEU cc_start: 0.8597 (mp) cc_final: 0.8388 (mt) REVERT: A 1542 MET cc_start: 0.7996 (mmm) cc_final: 0.7759 (mmm) REVERT: B 386 MET cc_start: 0.8524 (mmm) cc_final: 0.7219 (tmm) REVERT: B 530 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.7575 (t80) REVERT: B 570 TYR cc_start: 0.8701 (t80) cc_final: 0.8462 (t80) REVERT: B 1292 MET cc_start: 0.6611 (pp-130) cc_final: 0.6335 (mpp) REVERT: B 1376 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7865 (ttp) REVERT: B 1579 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8903 (tp) REVERT: C 386 MET cc_start: 0.8295 (mmm) cc_final: 0.7250 (tmm) REVERT: C 387 LEU cc_start: 0.8927 (tp) cc_final: 0.8723 (tp) REVERT: C 530 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7463 (t80) REVERT: C 653 MET cc_start: 0.8101 (mtm) cc_final: 0.7474 (tmm) REVERT: C 1173 ASP cc_start: 0.7742 (t0) cc_final: 0.6615 (t0) REVERT: C 1292 MET cc_start: 0.5692 (pp-130) cc_final: 0.4179 (ttp) REVERT: C 1352 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8458 (mt) REVERT: C 1415 GLN cc_start: 0.8327 (tp40) cc_final: 0.8052 (tp40) REVERT: D 386 MET cc_start: 0.8585 (mmm) cc_final: 0.7218 (tmm) REVERT: D 653 MET cc_start: 0.7877 (OUTLIER) cc_final: 0.7641 (tmm) REVERT: D 1028 LEU cc_start: 0.9279 (mt) cc_final: 0.9020 (tp) REVERT: D 1059 MET cc_start: 0.8614 (tpt) cc_final: 0.8401 (tpp) REVERT: D 1173 ASP cc_start: 0.7782 (t0) cc_final: 0.6624 (t0) REVERT: D 1292 MET cc_start: 0.5387 (pp-130) cc_final: 0.4002 (ttt) REVERT: D 1376 MET cc_start: 0.7858 (mtt) cc_final: 0.7628 (mtp) REVERT: D 1415 GLN cc_start: 0.8929 (tp40) cc_final: 0.8321 (tp40) outliers start: 133 outliers final: 65 residues processed: 540 average time/residue: 0.4863 time to fit residues: 449.7165 Evaluate side-chains 428 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 356 time to evaluate : 4.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1144 ARG Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1339 TYR Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1485 TYR Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 625 PHE Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1140 MET Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1339 TYR Chi-restraints excluded: chain B residue 1348 SER Chi-restraints excluded: chain B residue 1352 LEU Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1416 ILE Chi-restraints excluded: chain B residue 1523 THR Chi-restraints excluded: chain B residue 1547 VAL Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain B residue 1579 LEU Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain C residue 625 PHE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1276 VAL Chi-restraints excluded: chain C residue 1348 SER Chi-restraints excluded: chain C residue 1352 LEU Chi-restraints excluded: chain C residue 1416 ILE Chi-restraints excluded: chain C residue 1425 LEU Chi-restraints excluded: chain C residue 1549 LEU Chi-restraints excluded: chain C residue 1580 ILE Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 653 MET Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1276 VAL Chi-restraints excluded: chain D residue 1348 SER Chi-restraints excluded: chain D residue 1407 LEU Chi-restraints excluded: chain D residue 1416 ILE Chi-restraints excluded: chain D residue 1425 LEU Chi-restraints excluded: chain D residue 1437 LEU Chi-restraints excluded: chain D residue 1485 TYR Chi-restraints excluded: chain D residue 1547 VAL Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1569 ASP Chi-restraints excluded: chain D residue 1580 ILE 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: 40.0000 chunk 368 optimal weight: 0.9980 chunk 149 optimal weight: 60.0000 chunk 542 optimal weight: 0.7980 chunk 585 optimal weight: 0.0670 chunk 482 optimal weight: 8.9990 chunk 537 optimal weight: 0.6980 chunk 184 optimal weight: 0.6980 chunk 434 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 GLN A 736 ASN ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 GLN ** A1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 601 GLN B 682 ASN B 736 ASN ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 GLN B1482 ASN C 553 HIS C 601 GLN C 682 ASN C 736 ASN ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1162 GLN ** C1382 HIS ** 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** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 42652 Z= 0.183 Angle : 0.635 10.315 58284 Z= 0.325 Chirality : 0.039 0.166 7116 Planarity : 0.004 0.079 7384 Dihedral : 9.950 88.572 6906 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.19 % Favored : 91.72 % Rotamer: Outliers : 3.62 % Allowed : 11.72 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.09 % 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: -2.26 (0.10), residues: 5980 helix: -0.68 (0.08), residues: 3724 sheet: None (None), residues: 0 loop : -2.88 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C1572 HIS 0.011 0.001 HIS A1294 PHE 0.019 0.001 PHE B1278 TYR 0.022 0.002 TYR D1327 ARG 0.005 0.000 ARG A 483 *********************** 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 564 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 443 time to evaluate : 4.869 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: A 386 MET cc_start: 0.8486 (mmm) cc_final: 0.7197 (tmm) REVERT: A 530 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.7391 (t80) REVERT: A 653 MET cc_start: 0.7990 (mtt) cc_final: 0.7731 (tmm) REVERT: A 1053 MET cc_start: 0.8963 (ptt) cc_final: 0.8760 (ptp) REVERT: A 1318 LEU cc_start: 0.9129 (mt) cc_final: 0.8894 (mt) REVERT: A 1376 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7681 (mtp) REVERT: A 1564 ILE cc_start: 0.8586 (mt) cc_final: 0.8358 (mt) REVERT: B 386 MET cc_start: 0.8458 (mmm) cc_final: 0.7131 (tmm) REVERT: B 530 TYR cc_start: 0.7936 (OUTLIER) cc_final: 0.7505 (t80) REVERT: B 570 TYR cc_start: 0.8567 (t80) cc_final: 0.8328 (t80) REVERT: B 621 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8690 (tm) REVERT: B 653 MET cc_start: 0.7776 (mtm) cc_final: 0.7216 (tmm) REVERT: B 1053 MET cc_start: 0.8937 (ptt) cc_final: 0.8713 (ptp) REVERT: B 1292 MET cc_start: 0.6266 (pp-130) cc_final: 0.5932 (mpp) REVERT: B 1318 LEU cc_start: 0.9194 (mt) cc_final: 0.8899 (mt) REVERT: B 1352 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8447 (mt) REVERT: B 1376 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7713 (ttp) REVERT: B 1429 TRP cc_start: 0.8044 (t-100) cc_final: 0.7824 (t-100) REVERT: C 386 MET cc_start: 0.8272 (mmm) cc_final: 0.7225 (tmm) REVERT: C 530 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7421 (t80) REVERT: C 541 MET cc_start: 0.9132 (ptp) cc_final: 0.8911 (ptp) REVERT: C 625 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8475 (m-80) REVERT: C 653 MET cc_start: 0.8064 (mtm) cc_final: 0.7411 (tmm) REVERT: C 1028 LEU cc_start: 0.9289 (mt) cc_final: 0.9060 (tp) REVERT: C 1053 MET cc_start: 0.8964 (ptt) cc_final: 0.8746 (ptp) REVERT: C 1292 MET cc_start: 0.5546 (pp-130) cc_final: 0.3858 (ttt) REVERT: C 1415 GLN cc_start: 0.8262 (tp40) cc_final: 0.8059 (tp40) REVERT: C 1440 LEU cc_start: 0.9077 (tp) cc_final: 0.8851 (tp) REVERT: C 1542 MET cc_start: 0.7889 (mmm) cc_final: 0.7646 (mmm) REVERT: D 386 MET cc_start: 0.8506 (mmm) cc_final: 0.7200 (tmm) REVERT: D 530 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7630 (t80) REVERT: D 621 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8607 (tp) REVERT: D 1292 MET cc_start: 0.4898 (pp-130) cc_final: 0.3217 (ttt) REVERT: D 1376 MET cc_start: 0.7888 (mtt) cc_final: 0.7679 (mtp) REVERT: D 1415 GLN cc_start: 0.8704 (tp40) cc_final: 0.8070 (tp40) REVERT: D 1542 MET cc_start: 0.7880 (mmm) cc_final: 0.7621 (mmm) outliers start: 121 outliers final: 49 residues processed: 539 average time/residue: 0.4752 time to fit residues: 443.5507 Evaluate side-chains 457 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 398 time to evaluate : 4.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1376 MET Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1551 GLN Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1348 SER Chi-restraints excluded: chain B residue 1352 LEU Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1416 ILE Chi-restraints excluded: chain B residue 1458 ILE Chi-restraints excluded: chain B residue 1468 PHE Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 625 PHE Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 877 ASP Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 943 ASP Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1348 SER Chi-restraints excluded: chain C residue 1437 LEU Chi-restraints excluded: chain C residue 1549 LEU Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 877 ASP Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1348 SER Chi-restraints excluded: chain D residue 1437 LEU Chi-restraints excluded: chain D residue 1468 PHE Chi-restraints excluded: chain D residue 1547 VAL Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1559 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 535 optimal weight: 8.9990 chunk 407 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 258 optimal weight: 9.9990 chunk 364 optimal weight: 0.0470 chunk 544 optimal weight: 0.6980 chunk 576 optimal weight: 0.8980 chunk 284 optimal weight: 0.3980 chunk 515 optimal weight: 0.9990 chunk 155 optimal weight: 50.0000 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 682 ASN ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 ASN B 609 ASN ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 378 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 42652 Z= 0.168 Angle : 0.601 12.585 58284 Z= 0.305 Chirality : 0.039 0.211 7116 Planarity : 0.004 0.075 7384 Dihedral : 9.301 85.844 6904 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.51 % Favored : 91.42 % Rotamer: Outliers : 2.66 % Allowed : 13.73 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -1.62 (0.10), residues: 5980 helix: -0.08 (0.08), residues: 3736 sheet: None (None), residues: 0 loop : -2.82 (0.12), residues: 2244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D1572 HIS 0.011 0.001 HIS A1294 PHE 0.014 0.001 PHE B1538 TYR 0.023 0.001 TYR C 570 ARG 0.006 0.000 ARG B1483 *********************** REFINEMENT MACRO_CYCLE 4 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 536 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 447 time to evaluate : 4.828 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: A 386 MET cc_start: 0.8355 (mmm) cc_final: 0.7193 (tmm) REVERT: A 530 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.7518 (t80) REVERT: A 653 MET cc_start: 0.8126 (mtt) cc_final: 0.7682 (tmm) REVERT: A 1376 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7711 (mtp) REVERT: A 1415 GLN cc_start: 0.8712 (tp40) cc_final: 0.8415 (tp40) REVERT: B 386 MET cc_start: 0.8399 (mmm) cc_final: 0.7184 (tmm) REVERT: B 530 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7490 (t80) REVERT: B 541 MET cc_start: 0.9127 (ptp) cc_final: 0.8918 (ptp) REVERT: B 653 MET cc_start: 0.7761 (mtm) cc_final: 0.7114 (tmm) REVERT: B 952 VAL cc_start: 0.8700 (t) cc_final: 0.8475 (p) REVERT: B 1173 ASP cc_start: 0.7221 (t0) cc_final: 0.6056 (t0) REVERT: B 1290 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.5641 (m-10) REVERT: B 1292 MET cc_start: 0.6150 (pp-130) cc_final: 0.5647 (mpp) REVERT: B 1376 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7791 (ttp) REVERT: B 1433 ILE cc_start: 0.8507 (mt) cc_final: 0.8216 (mt) REVERT: C 386 MET cc_start: 0.8167 (mmm) cc_final: 0.6975 (tmm) REVERT: C 530 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7419 (t80) REVERT: C 653 MET cc_start: 0.7943 (mtm) cc_final: 0.7357 (tmm) REVERT: C 1292 MET cc_start: 0.5408 (pp-130) cc_final: 0.3445 (ttm) REVERT: C 1415 GLN cc_start: 0.8316 (tp40) cc_final: 0.8065 (tp40) REVERT: D 386 MET cc_start: 0.8356 (mmm) cc_final: 0.7195 (tmm) REVERT: D 530 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7543 (t80) REVERT: D 621 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8536 (tp) REVERT: D 1292 MET cc_start: 0.5130 (pp-130) cc_final: 0.3272 (ttt) REVERT: D 1376 MET cc_start: 0.8032 (mtt) cc_final: 0.7813 (mtp) REVERT: D 1415 GLN cc_start: 0.8701 (tp40) cc_final: 0.8081 (tp40) outliers start: 89 outliers final: 50 residues processed: 522 average time/residue: 0.4904 time to fit residues: 443.2127 Evaluate side-chains 453 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 395 time to evaluate : 4.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1376 MET Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1348 SER Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1468 PHE Chi-restraints excluded: chain B residue 1523 THR Chi-restraints excluded: chain B residue 1540 ILE Chi-restraints excluded: chain B residue 1551 GLN Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 877 ASP Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1348 SER Chi-restraints excluded: chain C residue 1350 LEU Chi-restraints excluded: chain C residue 1437 LEU Chi-restraints excluded: chain C residue 1444 LEU Chi-restraints excluded: chain C residue 1468 PHE Chi-restraints excluded: chain C residue 1577 SER Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 625 PHE Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1348 SER Chi-restraints excluded: chain D residue 1437 LEU Chi-restraints excluded: chain D residue 1468 PHE Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1551 GLN Chi-restraints excluded: chain D residue 1577 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 479 optimal weight: 2.9990 chunk 327 optimal weight: 0.8980 chunk 8 optimal weight: 40.0000 chunk 428 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 491 optimal weight: 5.9990 chunk 398 optimal weight: 1.9990 chunk 0 optimal weight: 50.0000 chunk 294 optimal weight: 0.7980 chunk 517 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 GLN ** A1382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1482 ASN C 609 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1162 GLN C1317 HIS C1382 HIS ** C1402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1551 GLN C1565 GLN D 378 ASN ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1162 GLN ** D1382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.3939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 42652 Z= 0.252 Angle : 0.626 11.595 58284 Z= 0.320 Chirality : 0.040 0.205 7116 Planarity : 0.004 0.070 7384 Dihedral : 9.116 79.890 6900 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.03 % Favored : 90.90 % Rotamer: Outliers : 3.14 % Allowed : 14.47 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -1.30 (0.11), residues: 5980 helix: 0.16 (0.08), residues: 3744 sheet: None (None), residues: 0 loop : -2.67 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1266 HIS 0.010 0.001 HIS A1294 PHE 0.033 0.001 PHE B1538 TYR 0.025 0.002 TYR B 570 ARG 0.003 0.000 ARG D1563 *********************** REFINEMENT MACRO_CYCLE 5 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 498 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 393 time to evaluate : 4.696 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: A 386 MET cc_start: 0.8408 (mmm) cc_final: 0.7302 (ttp) REVERT: A 530 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.7517 (t80) REVERT: A 653 MET cc_start: 0.8270 (mtt) cc_final: 0.7547 (tmm) REVERT: A 1376 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7628 (ttp) REVERT: A 1415 GLN cc_start: 0.8749 (tp40) cc_final: 0.8204 (tp40) REVERT: B 386 MET cc_start: 0.8441 (mmm) cc_final: 0.7263 (tmm) REVERT: B 530 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7617 (t80) REVERT: B 653 MET cc_start: 0.7814 (mtm) cc_final: 0.7226 (tmm) REVERT: B 952 VAL cc_start: 0.8706 (t) cc_final: 0.8502 (p) REVERT: B 1290 PHE cc_start: 0.6718 (OUTLIER) cc_final: 0.5629 (m-10) REVERT: B 1292 MET cc_start: 0.6334 (pp-130) cc_final: 0.5799 (mpp) REVERT: B 1376 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7691 (ttp) REVERT: B 1399 TYR cc_start: 0.8560 (t80) cc_final: 0.8295 (t80) REVERT: B 1551 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7443 (mt0) REVERT: C 386 MET cc_start: 0.8260 (mmm) cc_final: 0.7076 (tmm) REVERT: C 530 TYR cc_start: 0.7968 (OUTLIER) cc_final: 0.7472 (t80) REVERT: C 570 TYR cc_start: 0.8412 (t80) cc_final: 0.8196 (t80) REVERT: C 653 MET cc_start: 0.8188 (mtm) cc_final: 0.7494 (tmm) REVERT: C 1292 MET cc_start: 0.5986 (pp-130) cc_final: 0.4155 (ttt) REVERT: C 1415 GLN cc_start: 0.8541 (tp40) cc_final: 0.8211 (tp40) REVERT: C 1551 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7716 (mt0) REVERT: D 386 MET cc_start: 0.8394 (mmm) cc_final: 0.7354 (ttp) REVERT: D 463 ARG cc_start: 0.6737 (OUTLIER) cc_final: 0.6192 (mmp-170) REVERT: D 530 TYR cc_start: 0.7950 (OUTLIER) cc_final: 0.7622 (t80) REVERT: D 1292 MET cc_start: 0.5826 (pp-130) cc_final: 0.3778 (ttm) REVERT: D 1376 MET cc_start: 0.8101 (mtt) cc_final: 0.7839 (mtp) REVERT: D 1415 GLN cc_start: 0.8812 (tp40) cc_final: 0.8207 (tp40) outliers start: 105 outliers final: 63 residues processed: 480 average time/residue: 0.4659 time to fit residues: 393.3695 Evaluate side-chains 441 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 368 time to evaluate : 4.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1376 MET Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1444 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1550 ILE Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1140 MET Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1348 SER Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1440 LEU Chi-restraints excluded: chain B residue 1468 PHE Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1523 THR Chi-restraints excluded: chain B residue 1540 ILE Chi-restraints excluded: chain B residue 1551 GLN Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 877 ASP Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1348 SER Chi-restraints excluded: chain C residue 1433 ILE Chi-restraints excluded: chain C residue 1437 LEU Chi-restraints excluded: chain C residue 1444 LEU Chi-restraints excluded: chain C residue 1468 PHE Chi-restraints excluded: chain C residue 1549 LEU Chi-restraints excluded: chain C residue 1551 GLN Chi-restraints excluded: chain C residue 1577 SER Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 625 PHE Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1348 SER Chi-restraints excluded: chain D residue 1437 LEU Chi-restraints excluded: chain D residue 1468 PHE Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1577 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 193 optimal weight: 1.9990 chunk 518 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 338 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 576 optimal weight: 1.9990 chunk 478 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 190 optimal weight: 0.6980 chunk 302 optimal weight: 40.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 ASN A 609 ASN ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1243 GLN ** A1382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1402 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1243 GLN ** C1551 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 609 ASN ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1243 GLN ** D1382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 42652 Z= 0.206 Angle : 0.611 12.019 58284 Z= 0.310 Chirality : 0.039 0.212 7116 Planarity : 0.004 0.064 7384 Dihedral : 8.855 77.645 6900 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.98 % Favored : 90.95 % Rotamer: Outliers : 2.87 % Allowed : 15.40 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -1.05 (0.11), residues: 5980 helix: 0.36 (0.09), residues: 3756 sheet: None (None), residues: 0 loop : -2.59 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A1572 HIS 0.010 0.001 HIS A1294 PHE 0.013 0.001 PHE D1405 TYR 0.023 0.002 TYR D1327 ARG 0.003 0.000 ARG D1563 *********************** REFINEMENT MACRO_CYCLE 6 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 491 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 395 time to evaluate : 4.806 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: A 386 MET cc_start: 0.8402 (mmm) cc_final: 0.7131 (tmm) REVERT: A 530 TYR cc_start: 0.7848 (OUTLIER) cc_final: 0.7528 (t80) REVERT: A 653 MET cc_start: 0.8225 (mtt) cc_final: 0.7555 (tmm) REVERT: A 1376 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7479 (ttp) REVERT: A 1415 GLN cc_start: 0.8752 (tp40) cc_final: 0.8186 (tp40) REVERT: A 1551 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7637 (mm-40) REVERT: B 386 MET cc_start: 0.8467 (mmm) cc_final: 0.8258 (mmp) REVERT: B 530 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7628 (t80) REVERT: B 653 MET cc_start: 0.7903 (mtm) cc_final: 0.7223 (tmm) REVERT: B 952 VAL cc_start: 0.8643 (t) cc_final: 0.8428 (p) REVERT: B 1290 PHE cc_start: 0.6735 (OUTLIER) cc_final: 0.5606 (m-10) REVERT: B 1292 MET cc_start: 0.6338 (OUTLIER) cc_final: 0.5741 (mpp) REVERT: B 1376 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7680 (ttp) REVERT: B 1551 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7293 (mt0) REVERT: C 386 MET cc_start: 0.8252 (mmm) cc_final: 0.7003 (tmm) REVERT: C 530 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7468 (t80) REVERT: C 570 TYR cc_start: 0.8377 (t80) cc_final: 0.8161 (t80) REVERT: C 653 MET cc_start: 0.8172 (mtm) cc_final: 0.7387 (tmm) REVERT: C 1292 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.4201 (ttt) REVERT: C 1415 GLN cc_start: 0.8574 (tp40) cc_final: 0.8108 (tp40) REVERT: D 386 MET cc_start: 0.8395 (mmm) cc_final: 0.7225 (ttp) REVERT: D 530 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7649 (t80) REVERT: D 621 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8701 (tm) REVERT: D 1292 MET cc_start: 0.5789 (OUTLIER) cc_final: 0.3919 (ttt) REVERT: D 1415 GLN cc_start: 0.8758 (tp40) cc_final: 0.8135 (tp40) outliers start: 96 outliers final: 65 residues processed: 475 average time/residue: 0.4611 time to fit residues: 385.3164 Evaluate side-chains 446 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 368 time to evaluate : 4.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1376 MET Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1444 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1551 GLN Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1348 SER Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1440 LEU Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1468 PHE Chi-restraints excluded: chain B residue 1523 THR Chi-restraints excluded: chain B residue 1550 ILE Chi-restraints excluded: chain B residue 1551 GLN Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 877 ASP Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 943 ASP Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1348 SER Chi-restraints excluded: chain C residue 1437 LEU Chi-restraints excluded: chain C residue 1444 LEU Chi-restraints excluded: chain C residue 1468 PHE Chi-restraints excluded: chain C residue 1577 SER Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 625 PHE Chi-restraints excluded: chain D residue 664 LEU Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1348 SER Chi-restraints excluded: chain D residue 1437 LEU Chi-restraints excluded: chain D residue 1468 PHE Chi-restraints excluded: chain D residue 1547 VAL Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1577 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 555 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 328 optimal weight: 6.9990 chunk 421 optimal weight: 0.8980 chunk 326 optimal weight: 1.9990 chunk 485 optimal weight: 0.9990 chunk 322 optimal weight: 9.9990 chunk 574 optimal weight: 0.9990 chunk 359 optimal weight: 5.9990 chunk 350 optimal weight: 0.3980 chunk 265 optimal weight: 0.5980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1565 GLN ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1402 ASN B1482 ASN B1565 GLN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1402 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 42652 Z= 0.175 Angle : 0.602 13.111 58284 Z= 0.303 Chirality : 0.039 0.242 7116 Planarity : 0.003 0.062 7384 Dihedral : 8.529 73.412 6900 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.03 % Favored : 90.90 % Rotamer: Outliers : 2.63 % Allowed : 16.30 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -0.89 (0.11), residues: 5980 helix: 0.49 (0.09), residues: 3804 sheet: None (None), residues: 0 loop : -2.60 (0.12), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1266 HIS 0.010 0.001 HIS A1294 PHE 0.017 0.001 PHE B1538 TYR 0.031 0.001 TYR D 570 ARG 0.002 0.000 ARG C 463 *********************** REFINEMENT MACRO_CYCLE 7 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 500 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 412 time to evaluate : 4.589 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: A 386 MET cc_start: 0.8354 (mmm) cc_final: 0.7230 (ttp) REVERT: A 530 TYR cc_start: 0.7823 (OUTLIER) cc_final: 0.7515 (t80) REVERT: A 653 MET cc_start: 0.8168 (mtt) cc_final: 0.7546 (tmm) REVERT: A 1292 MET cc_start: 0.4283 (ttt) cc_final: 0.3824 (ttm) REVERT: A 1376 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7468 (ttp) REVERT: A 1415 GLN cc_start: 0.8662 (tp40) cc_final: 0.8203 (tp40) REVERT: A 1551 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7575 (mm-40) REVERT: B 386 MET cc_start: 0.8442 (mmm) cc_final: 0.8240 (mmp) REVERT: B 463 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.5723 (mmm160) REVERT: B 530 TYR cc_start: 0.7990 (OUTLIER) cc_final: 0.7619 (t80) REVERT: B 653 MET cc_start: 0.7848 (mtm) cc_final: 0.7202 (tmm) REVERT: B 952 VAL cc_start: 0.8593 (t) cc_final: 0.8376 (p) REVERT: B 1290 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5593 (m-10) REVERT: B 1292 MET cc_start: 0.6374 (OUTLIER) cc_final: 0.5748 (mpp) REVERT: B 1331 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.5762 (pmm-80) REVERT: B 1376 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7733 (ttp) REVERT: B 1551 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7211 (mt0) REVERT: C 386 MET cc_start: 0.8210 (mmm) cc_final: 0.6947 (tmm) REVERT: C 463 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.5674 (mmp-170) REVERT: C 530 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7417 (t80) REVERT: C 653 MET cc_start: 0.8087 (mtm) cc_final: 0.7318 (tmm) REVERT: C 1290 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.5603 (m-10) REVERT: C 1292 MET cc_start: 0.6081 (OUTLIER) cc_final: 0.5325 (mpp) REVERT: C 1415 GLN cc_start: 0.8543 (tp40) cc_final: 0.7964 (tp40) REVERT: C 1433 ILE cc_start: 0.8768 (mm) cc_final: 0.8533 (tt) REVERT: D 386 MET cc_start: 0.8349 (mmm) cc_final: 0.7088 (tmm) REVERT: D 463 ARG cc_start: 0.6151 (OUTLIER) cc_final: 0.5945 (mmm160) REVERT: D 530 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.7665 (t80) REVERT: D 621 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8797 (tm) REVERT: D 625 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8393 (m-80) REVERT: D 1292 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.3942 (ttt) REVERT: D 1415 GLN cc_start: 0.8729 (tp40) cc_final: 0.8119 (tp40) outliers start: 88 outliers final: 56 residues processed: 481 average time/residue: 0.4630 time to fit residues: 390.8502 Evaluate side-chains 451 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 376 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1376 MET Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1444 LEU Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1551 GLN Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1140 MET Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1331 ARG Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1444 LEU Chi-restraints excluded: chain B residue 1468 PHE Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1551 GLN Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain B residue 1593 LEU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 877 ASP Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1290 PHE Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1348 SER Chi-restraints excluded: chain C residue 1437 LEU Chi-restraints excluded: chain C residue 1468 PHE Chi-restraints excluded: chain C residue 1547 VAL Chi-restraints excluded: chain C residue 1577 SER Chi-restraints excluded: chain C residue 1593 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 625 PHE Chi-restraints excluded: chain D residue 877 ASP Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 943 ASP Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1348 SER Chi-restraints excluded: chain D residue 1437 LEU Chi-restraints excluded: chain D residue 1444 LEU Chi-restraints excluded: chain D residue 1468 PHE Chi-restraints excluded: chain D residue 1577 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 355 optimal weight: 1.9990 chunk 229 optimal weight: 4.9990 chunk 343 optimal weight: 7.9990 chunk 173 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 365 optimal weight: 10.0000 chunk 391 optimal weight: 0.6980 chunk 284 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 451 optimal weight: 8.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1382 HIS ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1162 GLN ** B1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1311 HIS B1382 HIS B1402 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1382 HIS D1402 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 42652 Z= 0.361 Angle : 0.698 13.403 58284 Z= 0.354 Chirality : 0.042 0.253 7116 Planarity : 0.004 0.065 7384 Dihedral : 8.919 63.526 6900 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.15 % Favored : 89.78 % Rotamer: Outliers : 3.32 % Allowed : 16.99 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -1.04 (0.11), residues: 5980 helix: 0.37 (0.08), residues: 3816 sheet: None (None), residues: 0 loop : -2.69 (0.12), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B1115 HIS 0.009 0.001 HIS A1294 PHE 0.037 0.002 PHE B1538 TYR 0.023 0.002 TYR A1327 ARG 0.005 0.001 ARG B1563 *********************** REFINEMENT MACRO_CYCLE 8 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 475 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 364 time to evaluate : 5.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.8456 (mmm) cc_final: 0.7306 (ttp) REVERT: A 530 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7671 (t80) REVERT: A 653 MET cc_start: 0.8188 (mtt) cc_final: 0.7501 (tmm) REVERT: A 1292 MET cc_start: 0.4732 (ttt) cc_final: 0.4250 (ttm) REVERT: A 1376 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7692 (ttp) REVERT: A 1415 GLN cc_start: 0.8873 (tp40) cc_final: 0.8259 (tp40) REVERT: B 530 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.7697 (t80) REVERT: B 653 MET cc_start: 0.8026 (mtm) cc_final: 0.7280 (tmm) REVERT: B 952 VAL cc_start: 0.8604 (t) cc_final: 0.8358 (p) REVERT: B 1290 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.5964 (m-10) REVERT: B 1292 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.4565 (tpp) REVERT: B 1331 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5296 (pmm-80) REVERT: B 1337 TYR cc_start: 0.7138 (t80) cc_final: 0.6577 (m-80) REVERT: B 1376 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7787 (ttp) REVERT: B 1399 TYR cc_start: 0.8429 (t80) cc_final: 0.8122 (t80) REVERT: C 386 MET cc_start: 0.8349 (mmm) cc_final: 0.7110 (ppp) REVERT: C 530 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.7510 (t80) REVERT: C 653 MET cc_start: 0.8217 (mtm) cc_final: 0.7441 (tmm) REVERT: C 1290 PHE cc_start: 0.6723 (OUTLIER) cc_final: 0.6147 (m-10) REVERT: C 1292 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.4289 (tpp) REVERT: C 1415 GLN cc_start: 0.8712 (tp40) cc_final: 0.8214 (tp40) REVERT: D 386 MET cc_start: 0.8485 (mmm) cc_final: 0.7214 (tmm) REVERT: D 530 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7687 (t80) REVERT: D 1059 MET cc_start: 0.8663 (tpp) cc_final: 0.8294 (tpp) REVERT: D 1292 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5529 (mpp) REVERT: D 1415 GLN cc_start: 0.8930 (tp40) cc_final: 0.8209 (tp40) outliers start: 111 outliers final: 67 residues processed: 453 average time/residue: 0.4769 time to fit residues: 379.9395 Evaluate side-chains 425 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 346 time to evaluate : 4.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1239 ILE Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1290 PHE Chi-restraints excluded: chain A residue 1316 ILE Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1376 MET Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1416 ILE Chi-restraints excluded: chain A residue 1549 LEU Chi-restraints excluded: chain A residue 1550 ILE Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1140 MET Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1331 ARG Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1523 THR Chi-restraints excluded: chain B residue 1547 VAL Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain B residue 1593 LEU Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 877 ASP Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1290 PHE Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1348 SER Chi-restraints excluded: chain C residue 1437 LEU Chi-restraints excluded: chain C residue 1444 LEU Chi-restraints excluded: chain C residue 1547 VAL Chi-restraints excluded: chain C residue 1577 SER Chi-restraints excluded: chain C residue 1593 LEU Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 491 SER Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 625 PHE Chi-restraints excluded: chain D residue 640 MET Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1348 SER Chi-restraints excluded: chain D residue 1416 ILE Chi-restraints excluded: chain D residue 1437 LEU Chi-restraints excluded: chain D residue 1444 LEU Chi-restraints excluded: chain D residue 1549 LEU Chi-restraints excluded: chain D residue 1577 SER Chi-restraints excluded: chain D residue 1593 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 522 optimal weight: 2.9990 chunk 550 optimal weight: 0.8980 chunk 502 optimal weight: 5.9990 chunk 535 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 chunk 233 optimal weight: 0.0010 chunk 420 optimal weight: 0.8980 chunk 164 optimal weight: 0.7980 chunk 483 optimal weight: 0.7980 chunk 506 optimal weight: 3.9990 chunk 533 optimal weight: 0.0970 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 42652 Z= 0.169 Angle : 0.625 13.415 58284 Z= 0.310 Chirality : 0.039 0.199 7116 Planarity : 0.003 0.058 7384 Dihedral : 8.416 63.541 6898 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.76 % Favored : 91.17 % Rotamer: Outliers : 2.45 % Allowed : 17.85 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -0.70 (0.11), residues: 5980 helix: 0.64 (0.09), residues: 3808 sheet: None (None), residues: 0 loop : -2.53 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D1572 HIS 0.011 0.001 HIS A1294 PHE 0.011 0.001 PHE A1574 TYR 0.023 0.001 TYR D 570 ARG 0.005 0.000 ARG D1127 *********************** REFINEMENT MACRO_CYCLE 9 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 471 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 389 time to evaluate : 4.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.7625 (t80) REVERT: A 653 MET cc_start: 0.8224 (mtt) cc_final: 0.7566 (tmm) REVERT: A 1276 VAL cc_start: 0.9006 (t) cc_final: 0.8716 (p) REVERT: A 1376 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.7488 (ttp) REVERT: A 1415 GLN cc_start: 0.8668 (tp40) cc_final: 0.8297 (tp40) REVERT: A 1551 GLN cc_start: 0.7793 (OUTLIER) cc_final: 0.7556 (mm-40) REVERT: B 530 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7627 (t80) REVERT: B 653 MET cc_start: 0.7880 (mtm) cc_final: 0.7190 (tmm) REVERT: B 952 VAL cc_start: 0.8543 (t) cc_final: 0.8323 (p) REVERT: B 1290 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.5454 (m-10) REVERT: B 1292 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5717 (mpp) REVERT: B 1331 ARG cc_start: 0.6086 (OUTLIER) cc_final: 0.5173 (pmm-80) REVERT: B 1376 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7674 (ttp) REVERT: B 1399 TYR cc_start: 0.8354 (t80) cc_final: 0.7855 (t80) REVERT: C 386 MET cc_start: 0.8260 (mmm) cc_final: 0.6990 (tmm) REVERT: C 530 TYR cc_start: 0.7896 (OUTLIER) cc_final: 0.7461 (t80) REVERT: C 653 MET cc_start: 0.8106 (mtm) cc_final: 0.7359 (tmm) REVERT: C 952 VAL cc_start: 0.8742 (t) cc_final: 0.8541 (p) REVERT: C 1292 MET cc_start: 0.6279 (OUTLIER) cc_final: 0.5558 (mpp) REVERT: C 1399 TYR cc_start: 0.8934 (t80) cc_final: 0.8487 (t80) REVERT: C 1433 ILE cc_start: 0.8918 (mm) cc_final: 0.8578 (tt) REVERT: D 386 MET cc_start: 0.8396 (mmm) cc_final: 0.7137 (tmm) REVERT: D 462 VAL cc_start: 0.5943 (OUTLIER) cc_final: 0.5556 (m) REVERT: D 463 ARG cc_start: 0.6062 (OUTLIER) cc_final: 0.5794 (mmm160) REVERT: D 530 TYR cc_start: 0.7957 (OUTLIER) cc_final: 0.7625 (t80) REVERT: D 625 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: D 1292 MET cc_start: 0.6133 (OUTLIER) cc_final: 0.5407 (mpp) REVERT: D 1415 GLN cc_start: 0.8728 (tp40) cc_final: 0.8064 (tp40) outliers start: 82 outliers final: 53 residues processed: 457 average time/residue: 0.4610 time to fit residues: 373.2025 Evaluate side-chains 441 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 373 time to evaluate : 4.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1376 MET Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1551 GLN Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1140 MET Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1331 ARG Chi-restraints excluded: chain B residue 1343 LEU Chi-restraints excluded: chain B residue 1369 VAL Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1468 PHE Chi-restraints excluded: chain B residue 1528 TYR Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain B residue 1593 LEU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 877 ASP Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1140 MET Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1348 SER Chi-restraints excluded: chain C residue 1468 PHE Chi-restraints excluded: chain C residue 1577 SER Chi-restraints excluded: chain C residue 1593 LEU Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 625 PHE Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1348 SER Chi-restraints excluded: chain D residue 1444 LEU Chi-restraints excluded: chain D residue 1468 PHE Chi-restraints excluded: chain D residue 1577 SER Chi-restraints excluded: chain D residue 1593 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 351 optimal weight: 0.9980 chunk 566 optimal weight: 0.9980 chunk 345 optimal weight: 0.9990 chunk 268 optimal weight: 0.9990 chunk 393 optimal weight: 2.9990 chunk 593 optimal weight: 0.6980 chunk 546 optimal weight: 2.9990 chunk 472 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 365 optimal weight: 9.9990 chunk 289 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1482 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 42652 Z= 0.205 Angle : 0.636 13.919 58284 Z= 0.315 Chirality : 0.040 0.285 7116 Planarity : 0.003 0.059 7384 Dihedral : 8.287 59.995 6898 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.63 % Favored : 91.30 % Rotamer: Outliers : 2.27 % Allowed : 18.54 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -0.61 (0.11), residues: 5980 helix: 0.70 (0.09), residues: 3808 sheet: None (None), residues: 0 loop : -2.48 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D1429 HIS 0.010 0.001 HIS A1294 PHE 0.024 0.001 PHE B1538 TYR 0.048 0.002 TYR D1399 ARG 0.005 0.000 ARG A1127 ********************** REFINEMENT MACRO_CYCLE 10 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 453 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 377 time to evaluate : 4.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7621 (t80) REVERT: A 653 MET cc_start: 0.8285 (mtt) cc_final: 0.7601 (tmm) REVERT: A 1276 VAL cc_start: 0.9007 (t) cc_final: 0.8727 (p) REVERT: A 1376 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7498 (ttp) REVERT: A 1415 GLN cc_start: 0.8720 (tp40) cc_final: 0.8343 (tp40) REVERT: B 530 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7627 (t80) REVERT: B 653 MET cc_start: 0.7900 (mtm) cc_final: 0.7215 (tmm) REVERT: B 1290 PHE cc_start: 0.6823 (OUTLIER) cc_final: 0.5477 (m-10) REVERT: B 1292 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.5783 (mpp) REVERT: B 1331 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.5244 (pmm-80) REVERT: B 1376 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.7515 (ttp) REVERT: B 1542 MET cc_start: 0.7898 (tpp) cc_final: 0.7649 (mmm) REVERT: C 386 MET cc_start: 0.8338 (mmm) cc_final: 0.7091 (tmm) REVERT: C 530 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7524 (t80) REVERT: C 653 MET cc_start: 0.8154 (mtm) cc_final: 0.7393 (tmm) REVERT: C 952 VAL cc_start: 0.8758 (t) cc_final: 0.8544 (p) REVERT: C 1290 PHE cc_start: 0.6865 (OUTLIER) cc_final: 0.5528 (m-10) REVERT: C 1292 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5563 (mpp) REVERT: C 1433 ILE cc_start: 0.8892 (mm) cc_final: 0.8671 (tt) REVERT: D 462 VAL cc_start: 0.5868 (OUTLIER) cc_final: 0.5484 (m) REVERT: D 463 ARG cc_start: 0.5969 (OUTLIER) cc_final: 0.5704 (mmm160) REVERT: D 530 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.7635 (t80) REVERT: D 625 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: D 1059 MET cc_start: 0.8583 (tpp) cc_final: 0.8376 (tpp) REVERT: D 1292 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.5527 (mpp) REVERT: D 1415 GLN cc_start: 0.8768 (tp40) cc_final: 0.8107 (tp40) outliers start: 76 outliers final: 54 residues processed: 442 average time/residue: 0.4681 time to fit residues: 365.6424 Evaluate side-chains 438 residues out of total 4952 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 369 time to evaluate : 4.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 530 TYR Chi-restraints excluded: chain A residue 676 VAL Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 989 ASN Chi-restraints excluded: chain A residue 1063 LEU Chi-restraints excluded: chain A residue 1140 MET Chi-restraints excluded: chain A residue 1235 LEU Chi-restraints excluded: chain A residue 1237 VAL Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1348 SER Chi-restraints excluded: chain A residue 1376 MET Chi-restraints excluded: chain A residue 1398 VAL Chi-restraints excluded: chain A residue 1468 PHE Chi-restraints excluded: chain A residue 1577 SER Chi-restraints excluded: chain A residue 1593 LEU Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 530 TYR Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1235 LEU Chi-restraints excluded: chain B residue 1237 VAL Chi-restraints excluded: chain B residue 1290 PHE Chi-restraints excluded: chain B residue 1292 MET Chi-restraints excluded: chain B residue 1331 ARG Chi-restraints excluded: chain B residue 1369 VAL Chi-restraints excluded: chain B residue 1376 MET Chi-restraints excluded: chain B residue 1468 PHE Chi-restraints excluded: chain B residue 1482 ASN Chi-restraints excluded: chain B residue 1523 THR Chi-restraints excluded: chain B residue 1559 ASP Chi-restraints excluded: chain B residue 1577 SER Chi-restraints excluded: chain B residue 1593 LEU Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain C residue 530 TYR Chi-restraints excluded: chain C residue 664 LEU Chi-restraints excluded: chain C residue 877 ASP Chi-restraints excluded: chain C residue 930 LEU Chi-restraints excluded: chain C residue 989 ASN Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1235 LEU Chi-restraints excluded: chain C residue 1237 VAL Chi-restraints excluded: chain C residue 1290 PHE Chi-restraints excluded: chain C residue 1292 MET Chi-restraints excluded: chain C residue 1348 SER Chi-restraints excluded: chain C residue 1350 LEU Chi-restraints excluded: chain C residue 1444 LEU Chi-restraints excluded: chain C residue 1468 PHE Chi-restraints excluded: chain C residue 1577 SER Chi-restraints excluded: chain C residue 1593 LEU Chi-restraints excluded: chain D residue 462 VAL Chi-restraints excluded: chain D residue 463 ARG Chi-restraints excluded: chain D residue 530 TYR Chi-restraints excluded: chain D residue 625 PHE Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 989 ASN Chi-restraints excluded: chain D residue 1140 MET Chi-restraints excluded: chain D residue 1235 LEU Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1292 MET Chi-restraints excluded: chain D residue 1348 SER Chi-restraints excluded: chain D residue 1444 LEU Chi-restraints excluded: chain D residue 1468 PHE Chi-restraints excluded: chain D residue 1577 SER Chi-restraints excluded: chain D residue 1593 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 596 random chunks: chunk 375 optimal weight: 0.8980 chunk 503 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 435 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 131 optimal weight: 0.5980 chunk 473 optimal weight: 9.9990 chunk 198 optimal weight: 0.0970 chunk 486 optimal weight: 0.0980 chunk 59 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1402 ASN ** B 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1317 HIS B1482 ASN ** C 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1402 ASN ** C1415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 980 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.124924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.103588 restraints weight = 172288.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.103596 restraints weight = 104759.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.103019 restraints weight = 75249.645| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 42652 Z= 0.168 Angle : 0.631 14.265 58284 Z= 0.309 Chirality : 0.040 0.311 7116 Planarity : 0.003 0.057 7384 Dihedral : 8.033 59.253 6898 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.48 % Favored : 91.45 % Rotamer: Outliers : 2.15 % Allowed : 18.48 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % 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: -0.53 (0.11), residues: 5980 helix: 0.73 (0.09), residues: 3820 sheet: None (None), residues: 0 loop : -2.38 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1572 HIS 0.010 0.001 HIS A1294 PHE 0.021 0.001 PHE B1538 TYR 0.043 0.001 TYR D1399 ARG 0.005 0.000 ARG B1483 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8763.46 seconds wall clock time: 160 minutes 5.20 seconds (9605.20 seconds total)