Starting phenix.real_space_refine (version: dev) on Fri Apr 8 09:56:55 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h67_0146/04_2022/6h67_0146_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h67_0146/04_2022/6h67_0146.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h67_0146/04_2022/6h67_0146_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h67_0146/04_2022/6h67_0146_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h67_0146/04_2022/6h67_0146_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h67_0146/04_2022/6h67_0146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h67_0146/04_2022/6h67_0146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h67_0146/04_2022/6h67_0146_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h67_0146/04_2022/6h67_0146_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 329": "NH1" <-> "NH2" Residue "A ARG 347": "NH1" <-> "NH2" Residue "A ARG 709": "NH1" <-> "NH2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 654": "NH1" <-> "NH2" Residue "B ARG 736": "NH1" <-> "NH2" Residue "B ARG 1063": "NH1" <-> "NH2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 33803 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 11565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1463, 11565 Classifications: {'peptide': 1463} Link IDs: {'PTRANS': 54, 'TRANS': 1403, 'PCIS': 5} Chain breaks: 6 Chain: "B" Number of atoms: 9329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1174, 9329 Classifications: {'peptide': 1174} Link IDs: {'PTRANS': 58, 'TRANS': 1114, 'PCIS': 1} Chain breaks: 2 Chain: "C" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2431 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 19, 'TRANS': 286} Chain: "D" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 431 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain breaks: 1 Chain: "E" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1734 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 199, 'PCIS': 1} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1348 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain breaks: 1 Chain: "H" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1051 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 466 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 792 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 351 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "M" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 856 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "N" Number of atoms: 1142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1142 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 9, 'TRANS': 134} Chain breaks: 2 Chain: "R" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 198 Classifications: {'RNA': 9} Modifications used: {'rna3p_pyr': 2, 'rna3p_pur': 7} Link IDs: {'rna3p': 8} Chain: "T" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 435 Unusual residues: {'TTD': 1} Classifications: {'undetermined': 1, 'DNA': 20} Link IDs: {'p': 1, None: 1, 'rna3p': 18} Not linked: pdbres=" DC T 17 " pdbres="TTD T 18 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "U" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 2, ' MG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 111.305 109.267 101.171 1.00 57.28 S ATOM 480 SG CYS A 65 111.225 107.909 104.535 1.00 57.22 S ATOM 535 SG CYS A 72 109.230 106.008 102.248 1.00 48.37 S ATOM 781 SG CYS A 102 72.376 142.106 93.649 1.00 81.33 S ATOM 806 SG CYS A 105 73.295 142.998 97.064 1.00 83.28 S ATOM 1589 SG CYS A 233 69.364 143.082 95.375 1.00 78.15 S ATOM 1611 SG CYS A 236 70.945 145.990 93.921 1.00 81.56 S ATOM 20188 SG CYS B1104 100.630 116.325 115.224 1.00 53.66 S ATOM 20214 SG CYS B1107 98.598 117.257 112.233 1.00 57.02 S ATOM 20361 SG CYS B1128 102.400 116.924 112.116 1.00 62.48 S ATOM 20389 SG CYS B1131 100.289 120.490 114.160 1.00 63.66 S ATOM 28797 SG CYS I 13 47.957 111.319 35.727 1.00101.00 S ATOM 28917 SG CYS I 30 47.903 114.925 37.930 1.00107.49 S ATOM 28938 SG CYS I 33 47.800 114.582 33.973 1.00104.04 S ATOM 29232 SG CYS J 7 86.471 40.653 90.468 1.00 20.99 S ATOM 29255 SG CYS J 10 86.656 37.976 92.927 1.00 19.72 S ATOM 29535 SG CYS J 45 83.156 38.324 91.947 1.00 23.88 S ATOM 29541 SG CYS J 46 85.901 36.289 89.911 1.00 24.70 S ATOM 30582 SG CYS L 31 112.904 63.745 62.725 1.00 50.30 S ATOM 30602 SG CYS L 34 113.889 61.524 59.881 1.00 56.50 S ATOM 30706 SG CYS L 48 115.807 64.511 60.636 1.00 74.79 S ATOM 30729 SG CYS L 51 113.118 64.587 57.934 1.00 71.02 S Time building chain proxies: 18.50, per 1000 atoms: 0.55 Number of scatterers: 33803 At special positions: 0 Unit cell: (160.06, 163.24, 163.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 6 29.99 S 166 16.00 P 44 15.00 Mg 1 11.99 O 6472 8.00 N 5861 7.00 C 21253 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.65 Conformation dependent library (CDL) restraints added in 5.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A 75 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 65 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 62 " pdb="ZN ZN A3001 " - pdb=" SG CYS A 72 " pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 105 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 102 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 236 " pdb="ZN ZN A3002 " - pdb=" SG CYS A 233 " pdb=" ZN B3001 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1104 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1107 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1131 " pdb="ZN ZN B3001 " - pdb=" SG CYS B1128 " pdb=" ZN I3001 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 13 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 33 " pdb="ZN ZN I3001 " - pdb=" SG CYS I 30 " pdb=" ZN J3001 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 7 " pdb="ZN ZN J3001 " - pdb=" SG CYS J 10 " pdb=" ZN L3001 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 51 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 48 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 31 " pdb="ZN ZN L3001 " - pdb=" SG CYS L 34 " Number of angles added : 27 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7790 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 137 helices and 35 sheets defined 28.0% alpha, 10.6% beta 20 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 12.38 Creating SS restraints... Processing helix chain 'A' and resid 21 through 27 removed outlier: 3.890A pdb=" N ASN A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 99 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.122A pdb=" N GLN A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 177 through 198 Processing helix chain 'A' and resid 210 through 226 Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'A' and resid 318 through 330 removed outlier: 3.702A pdb=" N LYS A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 removed outlier: 4.194A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 381 through 402 removed outlier: 3.710A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 438 removed outlier: 4.164A pdb=" N ASP A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 470 No H-bonds generated for 'chain 'A' and resid 467 through 470' Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 513 through 515 No H-bonds generated for 'chain 'A' and resid 513 through 515' Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 620 through 622 No H-bonds generated for 'chain 'A' and resid 620 through 622' Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 653 through 655 No H-bonds generated for 'chain 'A' and resid 653 through 655' Processing helix chain 'A' and resid 671 through 680 removed outlier: 3.804A pdb=" N SER A 675 " --> pdb=" O GLN A 671 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 699 removed outlier: 3.836A pdb=" N TYR A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 738 Processing helix chain 'A' and resid 783 through 786 No H-bonds generated for 'chain 'A' and resid 783 through 786' Processing helix chain 'A' and resid 794 through 800 Processing helix chain 'A' and resid 803 through 823 removed outlier: 3.977A pdb=" N ALA A 807 " --> pdb=" O PRO A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 839 through 849 removed outlier: 4.702A pdb=" N THR A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 862 Processing helix chain 'A' and resid 873 through 884 Processing helix chain 'A' and resid 888 through 910 removed outlier: 3.830A pdb=" N SER A 897 " --> pdb=" O ASP A 893 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 900 " --> pdb=" O THR A 896 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA A 902 " --> pdb=" O SER A 898 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLN A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 907 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 937 through 944 Processing helix chain 'A' and resid 992 through 1010 removed outlier: 3.829A pdb=" N MET A1000 " --> pdb=" O TYR A 996 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A1001 " --> pdb=" O PHE A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1025 removed outlier: 3.517A pdb=" N GLY A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N TYR A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1070 Processing helix chain 'A' and resid 1073 through 1080 Processing helix chain 'A' and resid 1082 through 1084 No H-bonds generated for 'chain 'A' and resid 1082 through 1084' Processing helix chain 'A' and resid 1092 through 1107 removed outlier: 3.660A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A1100 " --> pdb=" O LYS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1126 No H-bonds generated for 'chain 'A' and resid 1123 through 1126' Processing helix chain 'A' and resid 1138 through 1150 Processing helix chain 'A' and resid 1152 through 1156 Processing helix chain 'A' and resid 1163 through 1176 removed outlier: 3.925A pdb=" N LEU A1172 " --> pdb=" O ALA A1168 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1185 through 1194 removed outlier: 3.906A pdb=" N VAL A1193 " --> pdb=" O ALA A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1199 Processing helix chain 'A' and resid 1218 through 1225 removed outlier: 4.475A pdb=" N ARG A1223 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A1225 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1256 Processing helix chain 'A' and resid 1264 through 1266 No H-bonds generated for 'chain 'A' and resid 1264 through 1266' Processing helix chain 'A' and resid 1299 through 1302 No H-bonds generated for 'chain 'A' and resid 1299 through 1302' Processing helix chain 'A' and resid 1310 through 1317 Processing helix chain 'A' and resid 1321 through 1335 Processing helix chain 'A' and resid 1442 through 1452 Processing helix chain 'A' and resid 1485 through 1495 Processing helix chain 'A' and resid 1530 through 1532 No H-bonds generated for 'chain 'A' and resid 1530 through 1532' Processing helix chain 'A' and resid 1547 through 1552 Processing helix chain 'A' and resid 1554 through 1570 removed outlier: 3.910A pdb=" N ALA A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN A1568 " --> pdb=" O ASN A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1589 removed outlier: 4.488A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1600 through 1602 No H-bonds generated for 'chain 'A' and resid 1600 through 1602' Processing helix chain 'A' and resid 1609 through 1614 removed outlier: 3.539A pdb=" N SER A1614 " --> pdb=" O PHE A1610 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1626 Processing helix chain 'A' and resid 1637 through 1642 Processing helix chain 'A' and resid 1650 through 1653 removed outlier: 3.739A pdb=" N SER A1653 " --> pdb=" O GLY A1650 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1650 through 1653' Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 43 through 52 removed outlier: 3.968A pdb=" N LEU B 52 " --> pdb=" O SER B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 68 removed outlier: 4.367A pdb=" N LYS B 66 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 129 Processing helix chain 'B' and resid 177 through 182 Processing helix chain 'B' and resid 220 through 225 removed outlier: 3.699A pdb=" N ARG B 225 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.673A pdb=" N ILE B 293 " --> pdb=" O PHE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 Processing helix chain 'B' and resid 307 through 313 removed outlier: 4.167A pdb=" N GLY B 312 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 333 Processing helix chain 'B' and resid 335 through 338 No H-bonds generated for 'chain 'B' and resid 335 through 338' Processing helix chain 'B' and resid 346 through 356 removed outlier: 3.581A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 367 through 381 removed outlier: 3.806A pdb=" N ARG B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 406 through 434 Processing helix chain 'B' and resid 443 through 451 removed outlier: 4.016A pdb=" N MET B 451 " --> pdb=" O SER B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 467 Processing helix chain 'B' and resid 475 through 477 No H-bonds generated for 'chain 'B' and resid 475 through 477' Processing helix chain 'B' and resid 493 through 501 removed outlier: 4.296A pdb=" N PHE B 500 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG B 501 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 524 No H-bonds generated for 'chain 'B' and resid 522 through 524' Processing helix chain 'B' and resid 536 through 538 No H-bonds generated for 'chain 'B' and resid 536 through 538' Processing helix chain 'B' and resid 561 through 567 Processing helix chain 'B' and resid 598 through 614 removed outlier: 3.619A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 712 through 718 Processing helix chain 'B' and resid 762 through 764 No H-bonds generated for 'chain 'B' and resid 762 through 764' Processing helix chain 'B' and resid 791 through 794 No H-bonds generated for 'chain 'B' and resid 791 through 794' Processing helix chain 'B' and resid 835 through 838 Processing helix chain 'B' and resid 951 through 953 No H-bonds generated for 'chain 'B' and resid 951 through 953' Processing helix chain 'B' and resid 961 through 975 removed outlier: 3.863A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 1003 removed outlier: 3.971A pdb=" N GLN B 999 " --> pdb=" O TYR B 995 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS B1002 " --> pdb=" O GLU B 998 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B1003 " --> pdb=" O GLN B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1074 through 1081 Processing helix chain 'B' and resid 1089 through 1092 No H-bonds generated for 'chain 'B' and resid 1089 through 1092' Processing helix chain 'B' and resid 1180 through 1190 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.989A pdb=" N SER C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 242 through 250 removed outlier: 4.309A pdb=" N ARG C 246 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE C 247 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS C 250 " --> pdb=" O PHE C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 286 No H-bonds generated for 'chain 'C' and resid 283 through 286' Processing helix chain 'C' and resid 310 through 329 Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 83 through 91 removed outlier: 4.780A pdb=" N ARG D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 26 Processing helix chain 'E' and resid 32 through 35 No H-bonds generated for 'chain 'E' and resid 32 through 35' Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 121 No H-bonds generated for 'chain 'E' and resid 118 through 121' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 167 Processing helix chain 'E' and resid 185 through 188 No H-bonds generated for 'chain 'E' and resid 185 through 188' Processing helix chain 'F' and resid 56 through 70 Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 117 through 124 Processing helix chain 'F' and resid 148 through 150 No H-bonds generated for 'chain 'F' and resid 148 through 150' Processing helix chain 'G' and resid 51 through 53 No H-bonds generated for 'chain 'G' and resid 51 through 53' Processing helix chain 'G' and resid 57 through 64 Processing helix chain 'G' and resid 67 through 69 No H-bonds generated for 'chain 'G' and resid 67 through 69' Processing helix chain 'I' and resid 59 through 63 Processing helix chain 'J' and resid 15 through 17 No H-bonds generated for 'chain 'J' and resid 15 through 17' Processing helix chain 'J' and resid 19 through 28 removed outlier: 3.678A pdb=" N ASP J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 51 removed outlier: 4.216A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 51 through 53 No H-bonds generated for 'chain 'K' and resid 51 through 53' Processing helix chain 'K' and resid 70 through 81 removed outlier: 3.795A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 139 removed outlier: 3.702A pdb=" N LEU K 124 " --> pdb=" O GLY K 120 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR K 136 " --> pdb=" O GLU K 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 73 removed outlier: 3.763A pdb=" N SER M 73 " --> pdb=" O SER M 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 69 through 73' Processing helix chain 'N' and resid 150 through 153 No H-bonds generated for 'chain 'N' and resid 150 through 153' Processing sheet with id= A, first strand: chain 'A' and resid 77 through 80 Processing sheet with id= B, first strand: chain 'A' and resid 243 through 246 removed outlier: 3.864A pdb=" N LYS A 250 " --> pdb=" O ASP A 246 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 484 through 486 removed outlier: 6.980A pdb=" N LEU A 614 " --> pdb=" O SER A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 494 through 497 removed outlier: 7.513A pdb=" N ILE A 495 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LYS A 604 " --> pdb=" O ILE A 495 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL A 497 " --> pdb=" O LYS A 604 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG A 606 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 506 through 510 removed outlier: 3.999A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 749 through 751 Processing sheet with id= G, first strand: chain 'A' and resid 1238 through 1241 Processing sheet with id= H, first strand: chain 'A' and resid 1267 through 1272 removed outlier: 6.752A pdb=" N ARG A1295 " --> pdb=" O ASP A1268 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL A1270 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS A1293 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL A1272 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL A1291 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 71 through 73 removed outlier: 4.071A pdb=" N GLY B 159 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU B 139 " --> pdb=" O ASP B 157 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ASP B 157 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 141 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N VAL B 155 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 102 through 105 Processing sheet with id= K, first strand: chain 'B' and resid 194 through 196 Processing sheet with id= L, first strand: chain 'B' and resid 234 through 239 removed outlier: 6.254A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 652 through 655 removed outlier: 3.620A pdb=" N LYS B 660 " --> pdb=" O TYR B 655 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 740 through 744 removed outlier: 4.147A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN B 886 " --> pdb=" O SER B 902 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 1027 through 1033 removed outlier: 4.276A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 947 " --> pdb=" O ALA B 774 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 926 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE B 789 " --> pdb=" O VAL B 926 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N SER B 928 " --> pdb=" O ILE B 789 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 823 through 825 Processing sheet with id= Q, first strand: chain 'B' and resid 1102 through 1104 Processing sheet with id= R, first strand: chain 'B' and resid 1158 through 1160 Processing sheet with id= S, first strand: chain 'B' and resid 584 through 588 removed outlier: 3.612A pdb=" N GLY B 594 " --> pdb=" O VAL B 586 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 857 through 860 removed outlier: 6.747A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 52 through 56 Processing sheet with id= V, first strand: chain 'C' and resid 76 through 80 removed outlier: 4.494A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 231 through 235 Processing sheet with id= X, first strand: chain 'C' and resid 256 through 259 Processing sheet with id= Y, first strand: chain 'C' and resid 83 through 88 removed outlier: 6.555A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 161 through 163 Processing sheet with id= AA, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.932A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 152 through 155 removed outlier: 4.042A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE E 199 " --> pdb=" O LYS E 152 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AD, first strand: chain 'G' and resid 38 through 49 removed outlier: 3.791A pdb=" N GLY G 83 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N TRP G 125 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL G 81 " --> pdb=" O TRP G 125 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 147 through 149 removed outlier: 4.097A pdb=" N LEU G 147 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE G 153 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 100 through 105 removed outlier: 6.877A pdb=" N TYR H 115 " --> pdb=" O TYR H 102 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N PHE H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA H 113 " --> pdb=" O PHE H 104 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'K' and resid 47 through 49 Processing sheet with id= AH, first strand: chain 'M' and resid 37 through 44 Processing sheet with id= AI, first strand: chain 'M' and resid 77 through 81 removed outlier: 3.791A pdb=" N LEU M 80 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN M 89 " --> pdb=" O LEU M 80 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N GLU M 11 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU M 90 " --> pdb=" O GLU M 11 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N GLU M 13 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 11.238A pdb=" N LYS M 92 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 9.829A pdb=" N VAL M 15 " --> pdb=" O LYS M 92 " (cutoff:3.500A) 817 hydrogen bonds defined for protein. 2313 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 13.99 Time building geometry restraints manager: 14.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5586 1.31 - 1.44: 9050 1.44 - 1.57: 19565 1.57 - 1.69: 86 1.69 - 1.82: 263 Bond restraints: 34550 Sorted by residual: bond pdb=" C ILE A 495 " pdb=" N GLY A 496 " ideal model delta sigma weight residual 1.332 1.316 0.016 5.00e-03 4.00e+04 1.06e+01 bond pdb=" C6 TTD T 18 " pdb=" C6T TTD T 18 " ideal model delta sigma weight residual 1.580 1.629 -0.049 2.00e-02 2.50e+03 6.00e+00 bond pdb=" CA PRO C 252 " pdb=" C PRO C 252 " ideal model delta sigma weight residual 1.514 1.501 0.013 5.50e-03 3.31e+04 5.43e+00 bond pdb=" CB ARG B 714 " pdb=" CG ARG B 714 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.10e+00 bond pdb=" CG1 ILE B 412 " pdb=" CD1 ILE B 412 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.60e+00 ... (remaining 34545 not shown) Histogram of bond angle deviations from ideal: 84.01 - 94.04: 4 94.04 - 104.08: 664 104.08 - 114.12: 20457 114.12 - 124.16: 24924 124.16 - 134.19: 823 Bond angle restraints: 46872 Sorted by residual: angle pdb=" C ILE B 588 " pdb=" N ASP B 589 " pdb=" CA ASP B 589 " ideal model delta sigma weight residual 121.54 130.57 -9.03 1.91e+00 2.74e-01 2.23e+01 angle pdb=" N GLN A 671 " pdb=" CA GLN A 671 " pdb=" C GLN A 671 " ideal model delta sigma weight residual 110.80 119.87 -9.07 2.13e+00 2.20e-01 1.81e+01 angle pdb=" CA TYR C 227 " pdb=" CB TYR C 227 " pdb=" CG TYR C 227 " ideal model delta sigma weight residual 113.90 121.56 -7.66 1.80e+00 3.09e-01 1.81e+01 angle pdb=" N1 TTD T 18 " pdb=" C6 TTD T 18 " pdb=" C6T TTD T 18 " ideal model delta sigma weight residual 113.66 125.70 -12.04 3.00e+00 1.11e-01 1.61e+01 angle pdb=" CA LEU B1087 " pdb=" CB LEU B1087 " pdb=" CG LEU B1087 " ideal model delta sigma weight residual 116.30 130.09 -13.79 3.50e+00 8.16e-02 1.55e+01 ... (remaining 46867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.74: 20622 31.74 - 63.49: 254 63.49 - 95.23: 28 95.23 - 126.97: 0 126.97 - 158.71: 2 Dihedral angle restraints: 20906 sinusoidal: 8853 harmonic: 12053 Sorted by residual: dihedral pdb=" CA MET B 783 " pdb=" C MET B 783 " pdb=" N ASP B 784 " pdb=" CA ASP B 784 " ideal model delta harmonic sigma weight residual -180.00 -132.47 -47.53 0 5.00e+00 4.00e-02 9.03e+01 dihedral pdb=" CA ILE A 670 " pdb=" C ILE A 670 " pdb=" N GLN A 671 " pdb=" CA GLN A 671 " ideal model delta harmonic sigma weight residual 180.00 -146.11 -33.89 0 5.00e+00 4.00e-02 4.60e+01 dihedral pdb=" CA GLN A1500 " pdb=" C GLN A1500 " pdb=" N ILE A1501 " pdb=" CA ILE A1501 " ideal model delta harmonic sigma weight residual 180.00 146.59 33.41 0 5.00e+00 4.00e-02 4.47e+01 ... (remaining 20903 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 4780 0.095 - 0.190: 447 0.190 - 0.284: 15 0.284 - 0.379: 2 0.379 - 0.474: 1 Chirality restraints: 5245 Sorted by residual: chirality pdb=" C1R TTD T 18 " pdb=" C2R TTD T 18 " pdb=" N1T TTD T 18 " pdb=" O4R TTD T 18 " both_signs ideal model delta sigma weight residual False 2.44 1.96 0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CB VAL B1046 " pdb=" CA VAL B1046 " pdb=" CG1 VAL B1046 " pdb=" CG2 VAL B1046 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB VAL J 14 " pdb=" CA VAL J 14 " pdb=" CG1 VAL J 14 " pdb=" CG2 VAL J 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 5242 not shown) Planarity restraints: 5899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1R TTD T 18 " -0.034 2.00e-02 2.50e+03 3.66e-02 3.01e+01 pdb=" C2T TTD T 18 " -0.001 2.00e-02 2.50e+03 pdb=" C4T TTD T 18 " 0.028 2.00e-02 2.50e+03 pdb=" C5T TTD T 18 " -0.072 2.00e-02 2.50e+03 pdb=" C6T TTD T 18 " 0.067 2.00e-02 2.50e+03 pdb=" N1T TTD T 18 " 0.019 2.00e-02 2.50e+03 pdb=" N3T TTD T 18 " 0.001 2.00e-02 2.50e+03 pdb=" O2T TTD T 18 " -0.002 2.00e-02 2.50e+03 pdb=" O4T TTD T 18 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 783 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C MET B 783 " -0.046 2.00e-02 2.50e+03 pdb=" O MET B 783 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP B 784 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL G 41 " 0.040 5.00e-02 4.00e+02 6.14e-02 6.02e+00 pdb=" N PRO G 42 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 42 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 42 " 0.034 5.00e-02 4.00e+02 ... (remaining 5896 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 350 2.62 - 3.19: 27744 3.19 - 3.76: 50020 3.76 - 4.33: 71238 4.33 - 4.90: 115065 Nonbonded interactions: 264417 Sorted by model distance: nonbonded pdb=" O3' A R 10 " pdb="MG MG A3003 " model vdw 2.050 2.170 nonbonded pdb=" OD1 ASP A 627 " pdb="MG MG A3003 " model vdw 2.114 2.170 nonbonded pdb=" OD2 ASP A 631 " pdb="MG MG A3003 " model vdw 2.131 2.170 nonbonded pdb=" OD1 ASP A 631 " pdb="MG MG A3003 " model vdw 2.136 2.170 nonbonded pdb=" N CYS J 46 " pdb="ZN ZN J3001 " model vdw 2.214 2.310 ... (remaining 264412 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 6 6.06 5 P 44 5.49 5 Mg 1 5.21 5 S 166 5.16 5 C 21253 2.51 5 N 5861 2.21 5 O 6472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.980 Check model and map are aligned: 0.530 Convert atoms to be neutral: 0.310 Process input model: 97.250 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 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 : 0.006 0.081 34550 Z= 0.390 Angle : 0.874 13.786 46872 Z= 0.469 Chirality : 0.055 0.474 5245 Planarity : 0.007 0.061 5899 Dihedral : 10.792 158.713 13116 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.49 % Favored : 92.49 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -4.14 (0.10), residues: 4086 helix: -2.98 (0.10), residues: 1223 sheet: -2.44 (0.18), residues: 595 loop : -2.74 (0.11), residues: 2268 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1017 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1015 time to evaluate : 3.969 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 outliers start: 2 outliers final: 0 residues processed: 1017 average time/residue: 0.5064 time to fit residues: 797.3869 Evaluate side-chains 508 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 508 time to evaluate : 3.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 173 optimal weight: 0.0770 chunk 106 optimal weight: 8.9990 chunk 210 optimal weight: 1.9990 chunk 166 optimal weight: 10.0000 chunk 322 optimal weight: 0.5980 chunk 124 optimal weight: 8.9990 chunk 196 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 374 optimal weight: 2.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN A 470 HIS A 489 ASN A 525 ASN A 537 GLN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 ASN A 634 ASN A 639 GLN A 649 ASN A 673 HIS A 880 GLN A 886 ASN A 998 HIS A1036 ASN ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 ASN A1250 GLN A1447 GLN B 197 ASN B 243 GLN B 368 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 HIS ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 715 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 764 ASN B 770 ASN B 923 GLN B1082 HIS B1157 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 GLN E 99 HIS E 153 HIS E 179 GLN H 33 GLN ** H 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 21 ASN J 53 HIS K 64 GLN K 106 GLN M 71 GLN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 34550 Z= 0.186 Angle : 0.606 9.680 46872 Z= 0.313 Chirality : 0.044 0.345 5245 Planarity : 0.005 0.094 5899 Dihedral : 10.768 161.773 4918 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.06 (0.12), residues: 4086 helix: -1.59 (0.13), residues: 1220 sheet: -2.07 (0.19), residues: 590 loop : -2.30 (0.12), residues: 2276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 592 time to evaluate : 4.153 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 outliers start: 82 outliers final: 49 residues processed: 636 average time/residue: 0.5026 time to fit residues: 523.4915 Evaluate side-chains 524 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 475 time to evaluate : 4.148 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.3757 time to fit residues: 38.4918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 207 optimal weight: 7.9990 chunk 116 optimal weight: 10.0000 chunk 311 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 103 optimal weight: 0.2980 chunk 374 optimal weight: 0.8980 chunk 404 optimal weight: 8.9990 chunk 333 optimal weight: 20.0000 chunk 371 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 300 optimal weight: 8.9990 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN ** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 ASN A 901 ASN A 939 ASN A 998 HIS ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 128 GLN B 182 GLN B 197 ASN B 257 GLN B 368 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 702 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN E 146 HIS F 59 GLN F 100 GLN G 36 ASN G 119 HIS ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 34550 Z= 0.390 Angle : 0.715 10.618 46872 Z= 0.369 Chirality : 0.048 0.312 5245 Planarity : 0.006 0.097 5899 Dihedral : 10.848 159.746 4918 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer Outliers : 2.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.79 (0.12), residues: 4086 helix: -1.17 (0.14), residues: 1221 sheet: -2.19 (0.20), residues: 566 loop : -2.19 (0.12), residues: 2299 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 500 time to evaluate : 4.245 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 outliers start: 101 outliers final: 59 residues processed: 560 average time/residue: 0.4417 time to fit residues: 410.4450 Evaluate side-chains 500 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 441 time to evaluate : 3.916 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.3125 time to fit residues: 40.2745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 370 optimal weight: 1.9990 chunk 281 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 178 optimal weight: 0.1980 chunk 251 optimal weight: 2.9990 chunk 376 optimal weight: 0.5980 chunk 398 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 chunk 356 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 537 GLN A 620 ASN A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A 886 ASN A 998 HIS ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 368 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN B1171 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS G 36 ASN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 34550 Z= 0.175 Angle : 0.574 10.228 46872 Z= 0.293 Chirality : 0.043 0.332 5245 Planarity : 0.004 0.092 5899 Dihedral : 10.561 161.106 4918 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.28 (0.12), residues: 4086 helix: -0.63 (0.14), residues: 1213 sheet: -2.00 (0.20), residues: 565 loop : -1.91 (0.12), residues: 2308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 514 time to evaluate : 4.436 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 outliers start: 45 outliers final: 16 residues processed: 543 average time/residue: 0.4514 time to fit residues: 404.3274 Evaluate side-chains 463 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 447 time to evaluate : 3.975 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.3117 time to fit residues: 15.1372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 331 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 296 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 chunk 339 optimal weight: 30.0000 chunk 275 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 chunk 357 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 overall best weight: 6.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 ASN A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A 886 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 950 GLN A 998 HIS ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 ASN B 368 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 GLN ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN B1114 GLN B1171 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN ** C 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 HIS ** E 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 HIS ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.093 34550 Z= 0.468 Angle : 0.759 11.577 46872 Z= 0.390 Chirality : 0.050 0.305 5245 Planarity : 0.006 0.101 5899 Dihedral : 10.883 159.991 4918 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer Outliers : 2.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.62 (0.12), residues: 4086 helix: -0.88 (0.14), residues: 1196 sheet: -2.26 (0.19), residues: 587 loop : -2.10 (0.12), residues: 2303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 455 time to evaluate : 4.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 64 residues processed: 512 average time/residue: 0.4693 time to fit residues: 396.1734 Evaluate side-chains 482 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 418 time to evaluate : 4.188 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.3425 time to fit residues: 46.1759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 2.9990 chunk 358 optimal weight: 7.9990 chunk 78 optimal weight: 0.0070 chunk 233 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 398 optimal weight: 8.9990 chunk 330 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 33 optimal weight: 0.0980 chunk 131 optimal weight: 0.0670 chunk 209 optimal weight: 0.2980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 634 ASN A 730 GLN A 886 ASN A 998 HIS ** A1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 232 GLN E 32 GLN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 34550 Z= 0.173 Angle : 0.581 9.745 46872 Z= 0.297 Chirality : 0.043 0.332 5245 Planarity : 0.005 0.102 5899 Dihedral : 10.530 161.400 4918 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.08 (0.13), residues: 4086 helix: -0.36 (0.15), residues: 1207 sheet: -1.92 (0.20), residues: 560 loop : -1.83 (0.12), residues: 2319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 480 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 25 residues processed: 506 average time/residue: 0.4448 time to fit residues: 375.1308 Evaluate side-chains 454 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 429 time to evaluate : 4.067 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3502 time to fit residues: 21.6483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 227 optimal weight: 7.9990 chunk 291 optimal weight: 1.9990 chunk 225 optimal weight: 9.9990 chunk 335 optimal weight: 9.9990 chunk 222 optimal weight: 8.9990 chunk 397 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 242 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A 886 ASN A 998 HIS ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 HIS B 368 GLN ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 ASN ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 724 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 237 GLN D 30 HIS ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.141 34550 Z= 0.383 Angle : 0.685 10.127 46872 Z= 0.350 Chirality : 0.047 0.306 5245 Planarity : 0.006 0.114 5899 Dihedral : 10.640 160.353 4918 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.24 (0.13), residues: 4086 helix: -0.52 (0.15), residues: 1204 sheet: -2.06 (0.20), residues: 579 loop : -1.90 (0.12), residues: 2303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 439 time to evaluate : 3.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 40 residues processed: 472 average time/residue: 0.4514 time to fit residues: 355.8488 Evaluate side-chains 467 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 427 time to evaluate : 4.243 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3193 time to fit residues: 29.0898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 245 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 237 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 chunk 270 optimal weight: 0.7980 chunk 196 optimal weight: 0.8980 chunk 37 optimal weight: 0.0030 chunk 312 optimal weight: 0.0040 overall best weight: 0.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 730 GLN A 886 ASN A 901 ASN A 998 HIS ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 ASN B 987 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.188 34550 Z= 0.185 Angle : 0.587 12.453 46872 Z= 0.300 Chirality : 0.043 0.340 5245 Planarity : 0.005 0.118 5899 Dihedral : 10.393 161.415 4918 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.78 (0.13), residues: 4086 helix: -0.10 (0.15), residues: 1209 sheet: -1.74 (0.21), residues: 573 loop : -1.65 (0.13), residues: 2304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 468 time to evaluate : 4.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 478 average time/residue: 0.4442 time to fit residues: 355.2518 Evaluate side-chains 435 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 425 time to evaluate : 4.442 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3570 time to fit residues: 13.0812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 361 optimal weight: 0.2980 chunk 380 optimal weight: 6.9990 chunk 347 optimal weight: 9.9990 chunk 370 optimal weight: 1.9990 chunk 222 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 290 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 334 optimal weight: 0.0010 chunk 349 optimal weight: 3.9990 chunk 368 optimal weight: 1.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 HIS ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.378 34550 Z= 0.220 Angle : 0.586 19.961 46872 Z= 0.300 Chirality : 0.043 0.317 5245 Planarity : 0.005 0.128 5899 Dihedral : 10.223 161.202 4918 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.56 (0.13), residues: 4086 helix: 0.13 (0.15), residues: 1196 sheet: -1.59 (0.21), residues: 583 loop : -1.53 (0.13), residues: 2307 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 459 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 467 average time/residue: 0.4404 time to fit residues: 346.3212 Evaluate side-chains 438 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 427 time to evaluate : 4.019 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.3061 time to fit residues: 11.9782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 242 optimal weight: 8.9990 chunk 391 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 chunk 410 optimal weight: 9.9990 chunk 377 optimal weight: 8.9990 chunk 326 optimal weight: 0.0070 chunk 33 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 998 HIS ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 ASN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.161 34550 Z= 0.196 Angle : 0.587 12.729 46872 Z= 0.298 Chirality : 0.043 0.315 5245 Planarity : 0.005 0.136 5899 Dihedral : 10.173 161.409 4918 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.47 (0.13), residues: 4086 helix: 0.22 (0.15), residues: 1193 sheet: -1.51 (0.21), residues: 584 loop : -1.49 (0.13), residues: 2309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8172 Ramachandran restraints generated. 4086 Oldfield, 0 Emsley, 4086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 455 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 458 average time/residue: 0.4524 time to fit residues: 347.0921 Evaluate side-chains 439 residues out of total 3673 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 434 time to evaluate : 4.012 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3179 time to fit residues: 8.6637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 259 optimal weight: 0.6980 chunk 348 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 301 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 327 optimal weight: 0.0060 chunk 137 optimal weight: 4.9990 chunk 336 optimal weight: 10.0000 chunk 41 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN A 656 GLN ** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1453 HIS ** B 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 GLN ** C 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN ** M 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.157449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.132011 restraints weight = 63531.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.133838 restraints weight = 37708.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.134493 restraints weight = 26338.049| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 34550 Z= 0.184 Angle : 0.586 12.607 46872 Z= 0.294 Chirality : 0.043 0.314 5245 Planarity : 0.005 0.134 5899 Dihedral : 10.100 161.595 4918 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.34 (0.13), residues: 4086 helix: 0.35 (0.15), residues: 1175 sheet: -1.46 (0.21), residues: 585 loop : -1.41 (0.13), residues: 2326 =============================================================================== Job complete usr+sys time: 7546.69 seconds wall clock time: 138 minutes 8.71 seconds (8288.71 seconds total)