Starting phenix.real_space_refine (version: dev) on Tue Dec 13 19:59:28 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/12_2022/5zya_6915_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/12_2022/5zya_6915.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/12_2022/5zya_6915_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/12_2022/5zya_6915_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/12_2022/5zya_6915_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/12_2022/5zya_6915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/12_2022/5zya_6915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/12_2022/5zya_6915_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/12_2022/5zya_6915_updated.pdb" } resolution = 3.95 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= 0.007 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 "C ARG 495": "NH1" <-> "NH2" Residue "C ARG 558": "NH1" <-> "NH2" Residue "C ARG 590": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 736": "NH1" <-> "NH2" Residue "C ARG 822": "NH1" <-> "NH2" Residue "C ARG 827": "NH1" <-> "NH2" Residue "C ARG 831": "NH1" <-> "NH2" Residue "C ARG 939": "NH1" <-> "NH2" Residue "C ARG 948": "NH1" <-> "NH2" Residue "C ARG 1027": "NH1" <-> "NH2" Residue "C ARG 1045": "NH1" <-> "NH2" Residue "C ARG 1057": "NH1" <-> "NH2" Residue "C ARG 1075": "NH1" <-> "NH2" Residue "C ARG 1106": "NH1" <-> "NH2" Residue "C ARG 1245": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "A PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 429": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 718": "NH1" <-> "NH2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A ARG 895": "NH1" <-> "NH2" Residue "A ARG 1013": "NH1" <-> "NH2" Residue "A PHE 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 16957 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 539 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 3, 'TRANS': 62} Chain: "C" Number of atoms: 6438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6438 Classifications: {'peptide': 809} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 774} Chain breaks: 1 Chain: "D" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 645 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "A" Number of atoms: 9280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1183, 9280 Classifications: {'peptide': 1183} Link IDs: {'PCIS': 2, 'PTRANS': 58, 'TRANS': 1122} Chain breaks: 5 Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'9B0': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' ZN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7105 SG CYS D 23 30.112 90.456 66.528 1.00 68.38 S ATOM 7376 SG CYS D 58 33.151 91.184 64.701 1.00 63.42 S ATOM 7397 SG CYS D 61 29.986 92.741 63.750 1.00 65.46 S ATOM 7018 SG CYS D 11 43.982 98.304 55.595 1.00 71.87 S ATOM 7281 SG CYS D 46 46.263 97.192 59.934 1.00 62.04 S ATOM 7575 SG CYS D 85 45.777 95.371 56.868 1.00 67.32 S ATOM 7156 SG CYS D 30 38.525 81.746 57.804 1.00 52.14 S ATOM 7177 SG CYS D 33 37.070 80.142 54.160 1.00 47.74 S ATOM 7472 SG CYS D 72 39.458 78.230 56.015 1.00 44.18 S ATOM 7496 SG CYS D 75 40.699 80.609 53.666 1.00 43.95 S Time building chain proxies: 10.12, per 1000 atoms: 0.60 Number of scatterers: 16957 At special positions: 0 Unit cell: (132.2, 145.42, 125.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 K 1 19.00 S 102 16.00 O 3156 8.00 N 2895 7.00 C 10800 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=0, symmetry=0 Time building additional restraints: 7.13 Conformation dependent library (CDL) restraints added in 2.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 61 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 23 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 58 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 46 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 85 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 11 " pdb=" ZN D 203 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 33 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 72 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 30 " pdb="ZN ZN D 203 " - pdb=" SG CYS D 75 " Number of angles added : 6 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4012 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 25 sheets defined 31.3% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.57 Creating SS restraints... Processing helix chain 'B' and resid 28 through 45 Processing helix chain 'B' and resid 49 through 56 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'C' and resid 492 through 505 removed outlier: 4.834A pdb=" N LEU C 500 " --> pdb=" O LYS C 496 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU C 501 " --> pdb=" O ILE C 497 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU C 502 " --> pdb=" O MET C 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 521 Processing helix chain 'C' and resid 523 through 526 No H-bonds generated for 'chain 'C' and resid 523 through 526' Processing helix chain 'C' and resid 529 through 540 Proline residue: C 537 - end of helix Processing helix chain 'C' and resid 546 through 559 removed outlier: 3.516A pdb=" N LYS C 554 " --> pdb=" O HIS C 550 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ILE C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 579 Processing helix chain 'C' and resid 587 through 603 Processing helix chain 'C' and resid 606 through 612 Processing helix chain 'C' and resid 622 through 639 Processing helix chain 'C' and resid 642 through 652 Proline residue: C 646 - end of helix Processing helix chain 'C' and resid 658 through 675 Processing helix chain 'C' and resid 683 through 693 removed outlier: 5.598A pdb=" N HIS C 692 " --> pdb=" O GLU C 688 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLY C 693 " --> pdb=" O ILE C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 716 removed outlier: 4.306A pdb=" N ALA C 715 " --> pdb=" O ALA C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 737 removed outlier: 3.896A pdb=" N LEU C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARG C 736 " --> pdb=" O TRP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 751 removed outlier: 3.767A pdb=" N ALA C 749 " --> pdb=" O ALA C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 775 removed outlier: 4.192A pdb=" N LEU C 771 " --> pdb=" O ARG C 767 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE C 772 " --> pdb=" O GLU C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 795 Processing helix chain 'C' and resid 803 through 809 Processing helix chain 'C' and resid 811 through 817 Processing helix chain 'C' and resid 827 through 844 removed outlier: 4.139A pdb=" N LYS C 843 " --> pdb=" O GLU C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 852 Processing helix chain 'C' and resid 855 through 857 No H-bonds generated for 'chain 'C' and resid 855 through 857' Processing helix chain 'C' and resid 862 through 878 Processing helix chain 'C' and resid 889 through 901 Processing helix chain 'C' and resid 911 through 924 removed outlier: 7.469A pdb=" N LYS C 923 " --> pdb=" O ASN C 919 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG C 924 " --> pdb=" O ALA C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 929 through 940 Processing helix chain 'C' and resid 943 through 945 No H-bonds generated for 'chain 'C' and resid 943 through 945' Processing helix chain 'C' and resid 948 through 956 Processing helix chain 'C' and resid 959 through 963 Processing helix chain 'C' and resid 970 through 980 Processing helix chain 'C' and resid 987 through 1003 removed outlier: 3.923A pdb=" N SER C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL C1003 " --> pdb=" O ALA C 999 " (cutoff:3.500A) Processing helix chain 'C' and resid 1013 through 1025 Proline residue: C1018 - end of helix Proline residue: C1022 - end of helix removed outlier: 4.871A pdb=" N LYS C1025 " --> pdb=" O THR C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1029 through 1045 Processing helix chain 'C' and resid 1052 through 1067 removed outlier: 4.369A pdb=" N GLU C1064 " --> pdb=" O PHE C1060 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C1065 " --> pdb=" O GLU C1061 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU C1066 " --> pdb=" O LEU C1062 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N LYS C1067 " --> pdb=" O LEU C1063 " (cutoff:3.500A) Processing helix chain 'C' and resid 1071 through 1087 Processing helix chain 'C' and resid 1110 through 1122 Processing helix chain 'C' and resid 1128 through 1136 Processing helix chain 'C' and resid 1144 through 1158 Processing helix chain 'C' and resid 1160 through 1162 No H-bonds generated for 'chain 'C' and resid 1160 through 1162' Processing helix chain 'C' and resid 1167 through 1177 Proline residue: C1171 - end of helix Processing helix chain 'C' and resid 1182 through 1198 Processing helix chain 'C' and resid 1206 through 1219 removed outlier: 3.866A pdb=" N TYR C1214 " --> pdb=" O HIS C1210 " (cutoff:3.500A) Proline residue: C1217 - end of helix Processing helix chain 'C' and resid 1224 through 1241 Processing helix chain 'C' and resid 1243 through 1248 Processing helix chain 'C' and resid 1251 through 1253 No H-bonds generated for 'chain 'C' and resid 1251 through 1253' Processing helix chain 'C' and resid 1259 through 1274 removed outlier: 3.646A pdb=" N VAL C1264 " --> pdb=" O LYS C1260 " (cutoff:3.500A) Processing helix chain 'C' and resid 1277 through 1280 Processing helix chain 'C' and resid 1298 through 1300 No H-bonds generated for 'chain 'C' and resid 1298 through 1300' Processing helix chain 'D' and resid 24 through 26 No H-bonds generated for 'chain 'D' and resid 24 through 26' Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 809 through 824 Processing helix chain 'A' and resid 839 through 842 No H-bonds generated for 'chain 'A' and resid 839 through 842' Processing helix chain 'A' and resid 1135 through 1151 removed outlier: 4.528A pdb=" N SER A1150 " --> pdb=" O MET A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1161 through 1164 No H-bonds generated for 'chain 'A' and resid 1161 through 1164' Processing helix chain 'A' and resid 1187 through 1194 Processing helix chain 'A' and resid 1201 through 1214 removed outlier: 3.860A pdb=" N ILE A1211 " --> pdb=" O LYS A1207 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG A1212 " --> pdb=" O LEU A1208 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 39 through 42 removed outlier: 3.743A pdb=" N CYS D 40 " --> pdb=" O TYR D 71 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N TYR D 71 " --> pdb=" O CYS D 40 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.791A pdb=" N GLU A 39 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 54 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 64 through 66 removed outlier: 4.225A pdb=" N SER A 64 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET A 66 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE A 78 " --> pdb=" O LEU A 90 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 87 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 120 through 123 Processing sheet with id= E, first strand: chain 'A' and resid 165 through 167 removed outlier: 3.648A pdb=" N THR A 207 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 224 " --> pdb=" O PHE A 210 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLU A 212 " --> pdb=" O ARG A 222 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ARG A 222 " --> pdb=" O GLU A 212 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP A 214 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL A 220 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 235 through 237 removed outlier: 3.989A pdb=" N ILE A 236 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 249 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL A 248 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 292 through 294 removed outlier: 3.594A pdb=" N HIS A 293 " --> pdb=" O PHE A 300 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE A 300 " --> pdb=" O HIS A 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 775 through 780 removed outlier: 3.543A pdb=" N CYS A 427 " --> pdb=" O SER A 434 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 409 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 473 through 477 Processing sheet with id= J, first strand: chain 'A' and resid 533 through 537 removed outlier: 3.836A pdb=" N ARG A 525 " --> pdb=" O GLN A 518 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN A 518 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER A 507 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 574 through 576 removed outlier: 3.748A pdb=" N VAL A 564 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 554 " --> pdb=" O PHE A 566 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS A 546 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 640 through 643 removed outlier: 4.155A pdb=" N CYS A 641 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN A 666 " --> pdb=" O CYS A 641 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N TYR A 664 " --> pdb=" O VAL A 643 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 677 " --> pdb=" O LEU A 665 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE A 667 " --> pdb=" O LEU A 675 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 675 " --> pdb=" O ILE A 667 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.673A pdb=" N PHE A 702 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 712 " --> pdb=" O SER A 722 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 722 " --> pdb=" O VAL A 712 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 754 through 756 removed outlier: 6.453A pdb=" N ALA A 766 " --> pdb=" O GLU A 446 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU A 446 " --> pdb=" O ALA A 766 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 785 through 790 removed outlier: 7.587A pdb=" N ILE A 800 " --> pdb=" O ARG A 786 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N PHE A 788 " --> pdb=" O ILE A 798 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 798 " --> pdb=" O PHE A 788 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 803 " --> pdb=" O ALA A 863 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP A 878 " --> pdb=" O VAL A 868 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 943 through 945 removed outlier: 4.156A pdb=" N SER A 890 " --> pdb=" O GLY A 908 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA A 910 " --> pdb=" O ALA A 888 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ALA A 888 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 953 through 955 Processing sheet with id= R, first strand: chain 'A' and resid 990 through 994 removed outlier: 6.927A pdb=" N SER A1003 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE A 993 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE A1001 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA A1025 " --> pdb=" O TRP A1011 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG A1013 " --> pdb=" O ILE A1023 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N ILE A1023 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LYS A1015 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU A1021 " --> pdb=" O LYS A1015 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 1043 through 1045 removed outlier: 3.745A pdb=" N VAL A1055 " --> pdb=" O MET A1093 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET A1093 " --> pdb=" O VAL A1055 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG A1057 " --> pdb=" O VAL A1091 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N VAL A1091 " --> pdb=" O ARG A1057 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 1104 through 1107 Processing sheet with id= U, first strand: chain 'A' and resid 6 through 9 removed outlier: 6.743A pdb=" N ILE A1126 " --> pdb=" O LEU A 8 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 314 through 317 removed outlier: 3.981A pdb=" N ARG A 326 " --> pdb=" O THR A 314 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'A' and resid 336 through 342 removed outlier: 7.973A pdb=" N ALA A 350 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N MET A 339 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N PHE A 348 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A 341 " --> pdb=" O PHE A 346 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N PHE A 346 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 356 through 360 removed outlier: 3.815A pdb=" N LEU A 358 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP A 399 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLN A 360 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A 397 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 613 through 617 removed outlier: 3.864A pdb=" N SER A 629 " --> pdb=" O ILE A 616 " (cutoff:3.500A) 534 hydrogen bonds defined for protein. 1536 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: 6.05 Time building geometry restraints manager: 7.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4284 1.33 - 1.45: 3717 1.45 - 1.58: 9125 1.58 - 1.70: 6 1.70 - 1.83: 158 Bond restraints: 17290 Sorted by residual: bond pdb=" C10 9B0 C1401 " pdb=" C9 9B0 C1401 " ideal model delta sigma weight residual 1.697 1.420 0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" C6 9B0 C1401 " pdb=" C8 9B0 C1401 " ideal model delta sigma weight residual 1.514 1.720 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C1 9B0 C1401 " pdb=" C2 9B0 C1401 " ideal model delta sigma weight residual 1.592 1.396 0.196 2.00e-02 2.50e+03 9.56e+01 bond pdb=" C14 9B0 C1401 " pdb=" C16 9B0 C1401 " ideal model delta sigma weight residual 1.342 1.518 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" C17 9B0 C1401 " pdb=" C18 9B0 C1401 " ideal model delta sigma weight residual 1.345 1.516 -0.171 2.00e-02 2.50e+03 7.27e+01 ... (remaining 17285 not shown) Histogram of bond angle deviations from ideal: 58.60 - 75.54: 3 75.54 - 92.49: 1 92.49 - 109.44: 2357 109.44 - 126.39: 20844 126.39 - 143.34: 224 Bond angle restraints: 23429 Sorted by residual: angle pdb=" C13 9B0 C1401 " pdb=" C14 9B0 C1401 " pdb=" C15 9B0 C1401 " ideal model delta sigma weight residual 74.50 125.84 -51.34 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C17 9B0 C1401 " pdb=" C18 9B0 C1401 " pdb=" C19 9B0 C1401 " ideal model delta sigma weight residual 85.90 118.75 -32.85 3.00e+00 1.11e-01 1.20e+02 angle pdb=" C36 9B0 C1401 " pdb=" C37 9B0 C1401 " pdb=" C38 9B0 C1401 " ideal model delta sigma weight residual 112.96 143.34 -30.38 3.00e+00 1.11e-01 1.03e+02 angle pdb=" C11 9B0 C1401 " pdb=" C10 9B0 C1401 " pdb=" C9 9B0 C1401 " ideal model delta sigma weight residual 85.85 116.18 -30.33 3.00e+00 1.11e-01 1.02e+02 angle pdb=" C35 9B0 C1401 " pdb=" C34 9B0 C1401 " pdb=" N2 9B0 C1401 " ideal model delta sigma weight residual 108.92 138.11 -29.19 3.00e+00 1.11e-01 9.47e+01 ... (remaining 23424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 10382 35.22 - 70.44: 78 70.44 - 105.66: 7 105.66 - 140.88: 1 140.88 - 176.10: 2 Dihedral angle restraints: 10470 sinusoidal: 4243 harmonic: 6227 Sorted by residual: dihedral pdb=" CA GLN B 74 " pdb=" C GLN B 74 " pdb=" N PRO B 75 " pdb=" CA PRO B 75 " ideal model delta harmonic sigma weight residual -180.00 -143.25 -36.75 0 5.00e+00 4.00e-02 5.40e+01 dihedral pdb=" CA TYR C 719 " pdb=" C TYR C 719 " pdb=" N GLY C 720 " pdb=" CA GLY C 720 " ideal model delta harmonic sigma weight residual -180.00 -145.04 -34.96 0 5.00e+00 4.00e-02 4.89e+01 dihedral pdb=" CA ILE C 754 " pdb=" C ILE C 754 " pdb=" N PRO C 755 " pdb=" CA PRO C 755 " ideal model delta harmonic sigma weight residual 180.00 145.63 34.37 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 10467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.152: 2660 1.152 - 2.303: 0 2.303 - 3.455: 0 3.455 - 4.606: 1 4.606 - 5.758: 1 Chirality restraints: 2662 Sorted by residual: chirality pdb=" C6 9B0 C1401 " pdb=" C5 9B0 C1401 " pdb=" C7 9B0 C1401 " pdb=" C8 9B0 C1401 " both_signs ideal model delta sigma weight residual False -2.76 3.00 -5.76 2.00e-01 2.50e+01 8.29e+02 chirality pdb=" C34 9B0 C1401 " pdb=" C35 9B0 C1401 " pdb=" C40 9B0 C1401 " pdb=" N2 9B0 C1401 " both_signs ideal model delta sigma weight residual False -2.62 1.95 -4.57 2.00e-01 2.50e+01 5.22e+02 chirality pdb=" C8 9B0 C1401 " pdb=" C6 9B0 C1401 " pdb=" C9 9B0 C1401 " pdb=" O5 9B0 C1401 " both_signs ideal model delta sigma weight residual False 2.55 1.88 0.67 2.00e-01 2.50e+01 1.12e+01 ... (remaining 2659 not shown) Planarity restraints: 3022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 9B0 C1401 " -0.130 2.00e-02 2.50e+03 7.49e-02 5.61e+01 pdb=" C2 9B0 C1401 " 0.041 2.00e-02 2.50e+03 pdb=" O1 9B0 C1401 " 0.041 2.00e-02 2.50e+03 pdb=" O2 9B0 C1401 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 9B0 C1401 " 0.012 2.00e-02 2.50e+03 3.72e-02 1.73e+01 pdb=" C14 9B0 C1401 " -0.065 2.00e-02 2.50e+03 pdb=" C15 9B0 C1401 " 0.027 2.00e-02 2.50e+03 pdb=" C16 9B0 C1401 " 0.041 2.00e-02 2.50e+03 pdb=" C17 9B0 C1401 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 754 " -0.059 5.00e-02 4.00e+02 8.94e-02 1.28e+01 pdb=" N PRO C 755 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO C 755 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 755 " -0.049 5.00e-02 4.00e+02 ... (remaining 3019 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.37: 31 2.37 - 3.06: 10323 3.06 - 3.75: 29151 3.75 - 4.45: 43767 4.45 - 5.14: 71160 Nonbonded interactions: 154432 Sorted by model distance: nonbonded pdb=" O LEU C1251 " pdb=" CD1 LEU C1254 " model vdw 1.673 3.460 nonbonded pdb=" O ALA C 762 " pdb=" OG1 THR C 766 " model vdw 2.226 2.440 nonbonded pdb=" O GLN B 35 " pdb=" OG SER B 39 " model vdw 2.244 2.440 nonbonded pdb=" OG SER C 657 " pdb=" OE1 GLN C 659 " model vdw 2.249 2.440 nonbonded pdb=" O TYR C1167 " pdb=" OG1 THR C1170 " model vdw 2.252 2.440 ... (remaining 154427 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: 6 Type Number sf(0) Gaussians K 1 8.98 5 Zn 3 6.06 5 S 102 5.16 5 C 10800 2.51 5 N 2895 2.21 5 O 3156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.010 Extract box with map and model: 3.180 Check model and map are aligned: 0.270 Convert atoms to be neutral: 0.150 Process input model: 50.260 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5225 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 : 0.009 0.277 17290 Z= 0.598 Angle : 1.346 51.342 23429 Z= 0.678 Chirality : 0.156 5.758 2662 Planarity : 0.009 0.089 3022 Dihedral : 11.133 176.098 6458 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.10 % 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: -4.57 (0.15), residues: 2123 helix: -2.81 (0.14), residues: 682 sheet: -2.76 (0.21), residues: 445 loop : -3.28 (0.16), residues: 996 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 562 time to evaluate : 2.067 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 outliers start: 6 outliers final: 2 residues processed: 566 average time/residue: 0.3222 time to fit residues: 260.7574 Evaluate side-chains 324 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 322 time to evaluate : 2.095 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1432 time to fit residues: 3.4502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 192 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 23 HIS ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 67 ASN C 619 ASN C 662 HIS ** C 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 HIS C 821 HIS ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 ASN ** C1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN A 161 HIS A 194 ASN A 206 GLN A 231 HIS A 293 HIS ** A 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 411 GLN A 518 GLN A 636 GLN A 760 ASN A 775 ASN A 916 ASN A1052 ASN A1061 ASN A1160 HIS ** A1181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5847 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 17290 Z= 0.232 Angle : 0.873 28.107 23429 Z= 0.409 Chirality : 0.059 1.802 2662 Planarity : 0.006 0.074 3022 Dihedral : 7.736 141.979 2345 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 3.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.16), residues: 2123 helix: -1.29 (0.17), residues: 689 sheet: -2.20 (0.22), residues: 445 loop : -2.92 (0.17), residues: 989 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 376 time to evaluate : 2.083 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 outliers start: 70 outliers final: 28 residues processed: 419 average time/residue: 0.2815 time to fit residues: 177.1847 Evaluate side-chains 312 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 284 time to evaluate : 2.091 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1806 time to fit residues: 11.8479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 160 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 192 optimal weight: 3.9990 chunk 208 optimal weight: 0.1980 chunk 171 optimal weight: 0.6980 chunk 191 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 154 optimal weight: 40.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS C 547 GLN C 832 GLN ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1283 HIS ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN A 791 HIS A 804 HIS A 818 GLN A 885 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 17290 Z= 0.222 Angle : 0.831 25.678 23429 Z= 0.389 Chirality : 0.060 1.904 2662 Planarity : 0.005 0.059 3022 Dihedral : 7.659 161.884 2345 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -2.60 (0.17), residues: 2123 helix: -0.40 (0.19), residues: 697 sheet: -1.89 (0.23), residues: 439 loop : -2.63 (0.18), residues: 987 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 324 time to evaluate : 2.119 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: 40 outliers final: 20 residues processed: 350 average time/residue: 0.2658 time to fit residues: 143.8245 Evaluate side-chains 295 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 275 time to evaluate : 2.239 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1646 time to fit residues: 8.9459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 129 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 204 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 183 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN B 36 HIS ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1034 ASN ** C1184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 HIS A 666 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.6910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.140 17290 Z= 0.278 Angle : 0.833 26.007 23429 Z= 0.394 Chirality : 0.058 1.795 2662 Planarity : 0.005 0.069 3022 Dihedral : 7.451 151.300 2345 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -2.45 (0.17), residues: 2123 helix: -0.22 (0.19), residues: 685 sheet: -1.89 (0.22), residues: 445 loop : -2.53 (0.18), residues: 993 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 289 time to evaluate : 2.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 26 residues processed: 317 average time/residue: 0.2720 time to fit residues: 134.7550 Evaluate side-chains 281 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 255 time to evaluate : 1.967 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1527 time to fit residues: 10.2478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 152 optimal weight: 40.0000 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 547 GLN ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.7912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 17290 Z= 0.244 Angle : 0.814 25.476 23429 Z= 0.381 Chirality : 0.058 1.825 2662 Planarity : 0.005 0.076 3022 Dihedral : 7.456 156.463 2345 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -2.27 (0.18), residues: 2123 helix: -0.09 (0.20), residues: 704 sheet: -1.65 (0.24), residues: 426 loop : -2.52 (0.18), residues: 993 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 279 time to evaluate : 2.121 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: 44 outliers final: 21 residues processed: 309 average time/residue: 0.2710 time to fit residues: 130.2467 Evaluate side-chains 266 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 2.250 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1725 time to fit residues: 9.3166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 170 optimal weight: 0.9990 chunk 94 optimal weight: 0.0050 chunk 17 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.8309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 17290 Z= 0.189 Angle : 0.791 25.473 23429 Z= 0.364 Chirality : 0.057 1.813 2662 Planarity : 0.004 0.051 3022 Dihedral : 7.240 151.096 2345 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 1.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -2.08 (0.18), residues: 2123 helix: 0.09 (0.20), residues: 697 sheet: -1.45 (0.24), residues: 452 loop : -2.46 (0.19), residues: 974 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 281 time to evaluate : 2.175 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: 21 outliers final: 9 residues processed: 294 average time/residue: 0.2659 time to fit residues: 121.5743 Evaluate side-chains 263 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 254 time to evaluate : 2.032 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1566 time to fit residues: 5.4109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.0870 chunk 23 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 149 optimal weight: 30.0000 chunk 172 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 0.0570 chunk 94 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN A 231 HIS A 760 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.8885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 17290 Z= 0.225 Angle : 0.818 25.486 23429 Z= 0.378 Chirality : 0.058 1.820 2662 Planarity : 0.004 0.054 3022 Dihedral : 7.277 152.388 2345 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -2.07 (0.18), residues: 2123 helix: 0.00 (0.20), residues: 705 sheet: -1.32 (0.24), residues: 446 loop : -2.47 (0.18), residues: 972 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 264 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 20 residues processed: 283 average time/residue: 0.2775 time to fit residues: 122.9897 Evaluate side-chains 256 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 236 time to evaluate : 2.358 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1810 time to fit residues: 9.5488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.0370 chunk 122 optimal weight: 0.3980 chunk 61 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 139 optimal weight: 50.0000 chunk 101 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN A 988 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.9093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 17290 Z= 0.176 Angle : 0.810 25.491 23429 Z= 0.369 Chirality : 0.057 1.816 2662 Planarity : 0.004 0.057 3022 Dihedral : 7.117 148.183 2345 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -1.83 (0.18), residues: 2123 helix: 0.21 (0.20), residues: 699 sheet: -1.19 (0.25), residues: 445 loop : -2.31 (0.19), residues: 979 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 257 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 261 average time/residue: 0.2618 time to fit residues: 108.3786 Evaluate side-chains 248 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 241 time to evaluate : 2.081 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1555 time to fit residues: 4.9011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 9.9990 chunk 178 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 149 optimal weight: 30.0000 chunk 58 optimal weight: 0.0970 chunk 172 optimal weight: 10.0000 chunk 180 optimal weight: 0.9980 chunk 189 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 overall best weight: 0.7578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 988 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.9278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 17290 Z= 0.180 Angle : 0.825 25.484 23429 Z= 0.372 Chirality : 0.057 1.818 2662 Planarity : 0.004 0.065 3022 Dihedral : 7.087 147.587 2345 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -1.75 (0.18), residues: 2123 helix: 0.29 (0.20), residues: 687 sheet: -1.10 (0.24), residues: 470 loop : -2.29 (0.19), residues: 966 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 251 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 257 average time/residue: 0.2741 time to fit residues: 111.2353 Evaluate side-chains 246 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 239 time to evaluate : 2.161 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2060 time to fit residues: 5.4582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 211 optimal weight: 1.9990 chunk 194 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 129 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 492 GLN C 572 HIS ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 1.0032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 17290 Z= 0.308 Angle : 0.897 25.639 23429 Z= 0.423 Chirality : 0.060 1.824 2662 Planarity : 0.005 0.095 3022 Dihedral : 7.570 153.502 2345 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -2.13 (0.18), residues: 2123 helix: -0.20 (0.20), residues: 692 sheet: -1.14 (0.25), residues: 429 loop : -2.45 (0.18), residues: 1002 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4246 Ramachandran restraints generated. 2123 Oldfield, 0 Emsley, 2123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 241 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 249 average time/residue: 0.2744 time to fit residues: 107.6512 Evaluate side-chains 234 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 226 time to evaluate : 2.149 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1605 time to fit residues: 5.3843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 168 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 21 optimal weight: 0.0980 chunk 31 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1007 HIS ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.142343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.112437 restraints weight = 47521.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.113248 restraints weight = 28420.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.113990 restraints weight = 21409.617| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 1.0339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 17290 Z= 0.240 Angle : 0.859 25.545 23429 Z= 0.396 Chirality : 0.058 1.817 2662 Planarity : 0.005 0.079 3022 Dihedral : 7.414 149.454 2345 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: -2.06 (0.18), residues: 2123 helix: -0.09 (0.20), residues: 688 sheet: -1.16 (0.24), residues: 442 loop : -2.42 (0.18), residues: 993 =============================================================================== Job complete usr+sys time: 3420.08 seconds wall clock time: 63 minutes 9.47 seconds (3789.47 seconds total)