Starting phenix.real_space_refine (version: dev) on Wed Feb 22 08:15:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/02_2023/5zya_6915_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/02_2023/5zya_6915.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/02_2023/5zya_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_6915/02_2023/5zya_6915_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/02_2023/5zya_6915_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/02_2023/5zya_6915.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/02_2023/5zya_6915.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/02_2023/5zya_6915_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5zya_6915/02_2023/5zya_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 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-4877/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: 9.94, per 1000 atoms: 0.59 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: 6.59 Conformation dependent library (CDL) restraints added in 2.7 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: 2.68 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: 5.96 Time building geometry restraints manager: 7.16 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=" C6 9B0 C1401 " pdb=" C8 9B0 C1401 " ideal model delta sigma weight residual 1.493 1.720 -0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" C1 9B0 C1401 " pdb=" C2 9B0 C1401 " ideal model delta sigma weight residual 1.607 1.396 0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C10 9B0 C1401 " pdb=" C9 9B0 C1401 " ideal model delta sigma weight residual 1.622 1.420 0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C14 9B0 C1401 " pdb=" C16 9B0 C1401 " ideal model delta sigma weight residual 1.358 1.518 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" C17 9B0 C1401 " pdb=" C18 9B0 C1401 " ideal model delta sigma weight residual 1.356 1.516 -0.160 2.00e-02 2.50e+03 6.37e+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 74.55 125.84 -51.29 3.00e+00 1.11e-01 2.92e+02 angle pdb=" C17 9B0 C1401 " pdb=" C18 9B0 C1401 " pdb=" C19 9B0 C1401 " ideal model delta sigma weight residual 85.92 118.75 -32.83 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 85.83 116.18 -30.35 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 108.91 138.11 -29.20 3.00e+00 1.11e-01 9.48e+01 ... (remaining 23424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.15: 10245 26.15 - 52.29: 205 52.29 - 78.44: 13 78.44 - 104.59: 1 104.59 - 130.74: 6 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 - 1.153: 2660 1.153 - 2.305: 0 2.305 - 3.458: 0 3.458 - 4.610: 1 4.610 - 5.763: 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 -2.77 3.00 -5.76 2.00e-01 2.50e+01 8.30e+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 -2.61 1.95 -4.56 2.00e-01 2.50e+01 5.19e+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 1.13e+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: 0.410 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: 3.490 Check model and map are aligned: 0.240 Process input model: 47.900 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.130 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.390 ------------------------------------------------------------------------------- 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 0.227 17290 Z= 0.592 Angle : 1.346 51.292 23429 Z= 0.678 Chirality : 0.156 5.763 2662 Planarity : 0.009 0.089 3022 Dihedral : 11.242 130.736 6458 Min Nonbonded Distance : 1.673 Molprobity Statistics. All-atom Clashscore : 8.53 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 : 1.871 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: 0.3317 time to fit residues: 270.0774 Evaluate side-chains 324 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 322 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1571 time to fit residues: 3.5063 ------------------------------------------------------------------------------- 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 34 ASN ** 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: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5854 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 17290 Z= 0.229 Angle : 0.876 27.427 23429 Z= 0.410 Chirality : 0.059 1.815 2662 Planarity : 0.006 0.077 3022 Dihedral : 8.484 149.546 2345 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 3.73 % 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: -3.33 (0.16), residues: 2123 helix: -1.24 (0.18), residues: 688 sheet: -2.22 (0.22), residues: 443 loop : -2.91 (0.17), residues: 992 *********************** 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 445 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 376 time to evaluate : 2.102 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 outliers start: 69 outliers final: 28 residues processed: 420 average time/residue: 0.2971 time to fit residues: 187.0587 Evaluate side-chains 308 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 280 time to evaluate : 1.987 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1779 time to fit residues: 11.6523 ------------------------------------------------------------------------------- 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: 10.0000 chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 0.0770 chunk 131 optimal weight: 8.9990 chunk 53 optimal weight: 0.0270 chunk 192 optimal weight: 4.9990 chunk 208 optimal weight: 0.0980 chunk 171 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 154 optimal weight: 50.0000 overall best weight: 1.2400 ------------------------------------------------------------------------------- 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 669 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1184 HIS ** 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 A 791 HIS A 804 HIS A 818 GLN A 885 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1181 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.5364 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= 0.210 Angle : 0.829 26.094 23429 Z= 0.387 Chirality : 0.061 1.970 2662 Planarity : 0.005 0.058 3022 Dihedral : 7.921 128.924 2345 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 2.43 % 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: -2.58 (0.17), residues: 2123 helix: -0.38 (0.19), residues: 698 sheet: -1.88 (0.23), residues: 447 loop : -2.64 (0.18), residues: 978 *********************** 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 362 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 317 time to evaluate : 2.143 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: 22 residues processed: 343 average time/residue: 0.2778 time to fit residues: 147.1715 Evaluate side-chains 291 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 269 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1631 time to fit residues: 9.5073 ------------------------------------------------------------------------------- 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: 6.9990 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 HIS C 492 GLN ** C 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 666 ASN A 760 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1183 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.7459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.124 17290 Z= 0.317 Angle : 0.881 25.949 23429 Z= 0.422 Chirality : 0.061 1.828 2662 Planarity : 0.006 0.079 3022 Dihedral : 7.912 121.607 2345 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer Outliers : 3.46 % 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: -2.68 (0.17), residues: 2123 helix: -0.50 (0.19), residues: 705 sheet: -2.02 (0.23), residues: 437 loop : -2.63 (0.18), residues: 981 *********************** 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 356 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 292 time to evaluate : 2.092 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: 64 outliers final: 27 residues processed: 330 average time/residue: 0.2839 time to fit residues: 145.1257 Evaluate side-chains 271 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 244 time to evaluate : 2.116 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1757 time to fit residues: 11.5372 ------------------------------------------------------------------------------- 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: 0.9980 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 174 optimal weight: 4.9990 chunk 141 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 2.9990 chunk 183 optimal weight: 0.2980 chunk 51 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 GLN C 492 GLN C 547 GLN ** C 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 GLN ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.7978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 17290 Z= 0.210 Angle : 0.795 25.542 23429 Z= 0.368 Chirality : 0.058 1.875 2662 Planarity : 0.004 0.052 3022 Dihedral : 7.673 122.440 2345 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % 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: -2.24 (0.18), residues: 2123 helix: -0.02 (0.20), residues: 694 sheet: -1.72 (0.23), residues: 446 loop : -2.47 (0.19), residues: 983 *********************** 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 320 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 280 time to evaluate : 2.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 16 residues processed: 305 average time/residue: 0.2951 time to fit residues: 141.0429 Evaluate side-chains 264 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 248 time to evaluate : 2.043 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1621 time to fit residues: 7.8386 ------------------------------------------------------------------------------- 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: 0.9980 chunk 184 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 205 optimal weight: 0.3980 chunk 170 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN ** C 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.8320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.073 17290 Z= 0.177 Angle : 0.780 25.635 23429 Z= 0.356 Chirality : 0.058 1.868 2662 Planarity : 0.004 0.048 3022 Dihedral : 7.436 126.676 2345 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 1.24 % 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: -2.04 (0.18), residues: 2123 helix: 0.08 (0.20), residues: 700 sheet: -1.41 (0.24), residues: 453 loop : -2.41 (0.19), residues: 970 *********************** 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 309 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 286 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 301 average time/residue: 0.2838 time to fit residues: 132.3998 Evaluate side-chains 261 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 251 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1616 time to fit residues: 6.1136 ------------------------------------------------------------------------------- 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: 0.0370 chunk 23 optimal weight: 0.8980 chunk 116 optimal weight: 10.0000 chunk 149 optimal weight: 50.0000 chunk 172 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 204 optimal weight: 8.9990 chunk 127 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 662 HIS ** C 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 231 HIS 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: 0.6789 moved from start: 0.8598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 17290 Z= 0.186 Angle : 0.802 25.705 23429 Z= 0.364 Chirality : 0.058 1.869 2662 Planarity : 0.004 0.052 3022 Dihedral : 7.350 126.886 2345 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 1.40 % 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: -1.88 (0.18), residues: 2123 helix: 0.18 (0.20), residues: 696 sheet: -1.31 (0.23), residues: 482 loop : -2.30 (0.19), residues: 945 *********************** 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 297 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 271 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 286 average time/residue: 0.2704 time to fit residues: 120.5018 Evaluate side-chains 263 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 251 time to evaluate : 2.110 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1666 time to fit residues: 6.6129 ------------------------------------------------------------------------------- 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: 0.7980 chunk 122 optimal weight: 0.0970 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 101 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 chunk 185 optimal weight: 7.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.8943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.082 17290 Z= 0.197 Angle : 0.806 25.655 23429 Z= 0.366 Chirality : 0.057 1.865 2662 Planarity : 0.004 0.047 3022 Dihedral : 7.324 124.304 2345 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 1.19 % 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: -1.84 (0.18), residues: 2123 helix: 0.15 (0.20), residues: 700 sheet: -1.18 (0.24), residues: 451 loop : -2.29 (0.19), residues: 972 *********************** 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 279 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 257 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 270 average time/residue: 0.2756 time to fit residues: 117.0032 Evaluate side-chains 259 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 244 time to evaluate : 1.921 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1538 time to fit residues: 7.1279 ------------------------------------------------------------------------------- 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: 0.9990 chunk 190 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 149 optimal weight: 50.0000 chunk 58 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 189 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 HIS ** C 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.9841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 17290 Z= 0.279 Angle : 0.880 25.483 23429 Z= 0.413 Chirality : 0.060 1.844 2662 Planarity : 0.005 0.075 3022 Dihedral : 7.639 121.878 2345 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer Outliers : 1.03 % 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: -0.12 (0.20), residues: 698 sheet: -1.18 (0.24), residues: 437 loop : -2.42 (0.18), residues: 988 *********************** 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 263 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 244 time to evaluate : 2.151 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 255 average time/residue: 0.2840 time to fit residues: 112.6137 Evaluate side-chains 233 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 222 time to evaluate : 2.060 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1972 time to fit residues: 6.6328 ------------------------------------------------------------------------------- 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: 2.9990 chunk 122 optimal weight: 0.0770 chunk 95 optimal weight: 4.9990 chunk 139 optimal weight: 0.0040 chunk 211 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.7954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1194 HIS ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6948 moved from start: 0.9997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 17290 Z= 0.194 Angle : 0.851 25.749 23429 Z= 0.387 Chirality : 0.059 1.865 2662 Planarity : 0.004 0.049 3022 Dihedral : 7.451 122.698 2345 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.38 % 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: -1.86 (0.18), residues: 2123 helix: 0.00 (0.20), residues: 701 sheet: -0.93 (0.25), residues: 424 loop : -2.32 (0.18), residues: 998 ********************** 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 253 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 246 time to evaluate : 1.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 249 average time/residue: 0.2687 time to fit residues: 104.9017 Evaluate side-chains 229 residues out of total 1851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 224 time to evaluate : 2.089 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1682 time to fit residues: 4.4095 ------------------------------------------------------------------------------- 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: 8.9990 chunk 51 optimal weight: 0.0980 chunk 155 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 172 optimal weight: 2.9990 chunk 21 optimal weight: 0.0050 chunk 31 optimal weight: 2.9990 chunk 147 optimal weight: 30.0000 overall best weight: 2.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1034 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1194 HIS ** C1277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 ASN ** A1087 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1160 HIS ** 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 = 0.4238 r_free = 0.4238 target = 0.142775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.113563 restraints weight = 47747.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.113343 restraints weight = 30161.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.114704 restraints weight = 24123.073| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 1.0322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 17290 Z= 0.245 Angle : 0.863 25.577 23429 Z= 0.398 Chirality : 0.059 1.865 2662 Planarity : 0.005 0.061 3022 Dihedral : 7.531 126.382 2345 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % 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: -1.92 (0.18), residues: 2123 helix: -0.09 (0.20), residues: 701 sheet: -0.98 (0.24), residues: 440 loop : -2.32 (0.18), residues: 982 =============================================================================== Job complete usr+sys time: 3446.46 seconds wall clock time: 63 minutes 23.66 seconds (3803.66 seconds total)