Starting phenix.real_space_refine on Wed Feb 21 18:49:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed7_28031/02_2024/8ed7_28031_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed7_28031/02_2024/8ed7_28031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed7_28031/02_2024/8ed7_28031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed7_28031/02_2024/8ed7_28031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed7_28031/02_2024/8ed7_28031_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ed7_28031/02_2024/8ed7_28031_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 226 5.16 5 C 20456 2.51 5 N 5325 2.21 5 O 5511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31518 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 7736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 7736 Classifications: {'peptide': 954} Link IDs: {'PTRANS': 33, 'TRANS': 920} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 7760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7760 Classifications: {'peptide': 957} Link IDs: {'PTRANS': 33, 'TRANS': 923} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 7760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 957, 7760 Classifications: {'peptide': 957} Link IDs: {'PTRANS': 33, 'TRANS': 923} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 7766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7766 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 33, 'TRANS': 924} Chain breaks: 6 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 78 Unusual residues: {'9Z9': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'9Z9': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'9Z9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.44, per 1000 atoms: 0.55 Number of scatterers: 31518 At special positions: 0 Unit cell: (140.175, 140.175, 152.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 226 16.00 O 5511 8.00 N 5325 7.00 C 20456 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: 12.05 Conformation dependent library (CDL) restraints added in 5.2 seconds 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 185 helices and 4 sheets defined 58.7% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.32 Creating SS restraints... Processing helix chain 'A' and resid 166 through 175 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 228 through 243 removed outlier: 3.791A pdb=" N ALA A 241 " --> pdb=" O LYS A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 309 through 321 Processing helix chain 'A' and resid 343 through 354 removed outlier: 3.969A pdb=" N SER A 347 " --> pdb=" O PRO A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 367 No H-bonds generated for 'chain 'A' and resid 365 through 367' Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 399 through 401 No H-bonds generated for 'chain 'A' and resid 399 through 401' Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 440 through 452 removed outlier: 3.539A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 Processing helix chain 'A' and resid 469 through 474 Processing helix chain 'A' and resid 487 through 497 removed outlier: 3.511A pdb=" N VAL A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 514 through 517 No H-bonds generated for 'chain 'A' and resid 514 through 517' Processing helix chain 'A' and resid 520 through 528 Processing helix chain 'A' and resid 537 through 544 Processing helix chain 'A' and resid 557 through 568 Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 637 through 647 Processing helix chain 'A' and resid 651 through 658 Processing helix chain 'A' and resid 664 through 684 Processing helix chain 'A' and resid 691 through 716 removed outlier: 4.655A pdb=" N ASN A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS A 697 " --> pdb=" O GLN A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 724 Processing helix chain 'A' and resid 730 through 732 No H-bonds generated for 'chain 'A' and resid 730 through 732' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 750 No H-bonds generated for 'chain 'A' and resid 747 through 750' Processing helix chain 'A' and resid 753 through 763 Processing helix chain 'A' and resid 775 through 782 Processing helix chain 'A' and resid 784 through 787 No H-bonds generated for 'chain 'A' and resid 784 through 787' Processing helix chain 'A' and resid 862 through 868 Processing helix chain 'A' and resid 871 through 894 Processing helix chain 'A' and resid 903 through 924 Processing helix chain 'A' and resid 931 through 938 removed outlier: 3.689A pdb=" N VAL A 935 " --> pdb=" O LEU A 931 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 936 " --> pdb=" O LEU A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 961 Processing helix chain 'A' and resid 965 through 992 removed outlier: 4.204A pdb=" N ILE A 980 " --> pdb=" O CYS A 976 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR A 981 " --> pdb=" O VAL A 977 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LEU A 986 " --> pdb=" O TRP A 982 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU A 987 " --> pdb=" O TYR A 983 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N ASP A 988 " --> pdb=" O ILE A 984 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A 992 " --> pdb=" O ASP A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1032 removed outlier: 3.512A pdb=" N VAL A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP A1009 " --> pdb=" O LYS A1005 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1045 No H-bonds generated for 'chain 'A' and resid 1042 through 1045' Processing helix chain 'A' and resid 1048 through 1054 removed outlier: 4.053A pdb=" N ILE A1054 " --> pdb=" O PRO A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1102 Proline residue: A1092 - end of helix removed outlier: 3.559A pdb=" N ALA A1102 " --> pdb=" O LEU A1099 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1116 Processing helix chain 'A' and resid 1119 through 1141 removed outlier: 4.598A pdb=" N TYR A1134 " --> pdb=" O LYS A1130 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLN A1135 " --> pdb=" O PHE A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1150 No H-bonds generated for 'chain 'A' and resid 1148 through 1150' Processing helix chain 'A' and resid 1152 through 1162 removed outlier: 3.679A pdb=" N MET A1158 " --> pdb=" O SER A1154 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE A1159 " --> pdb=" O HIS A1155 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE A1160 " --> pdb=" O MET A1156 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N HIS A1162 " --> pdb=" O MET A1158 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1214 removed outlier: 3.500A pdb=" N SER A1214 " --> pdb=" O ASP A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1239 Processing helix chain 'B' and resid 166 through 175 Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 229 through 243 removed outlier: 3.535A pdb=" N LYS B 243 " --> pdb=" O ASP B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 321 Processing helix chain 'B' and resid 343 through 354 removed outlier: 3.846A pdb=" N SER B 347 " --> pdb=" O PRO B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 399 through 401 No H-bonds generated for 'chain 'B' and resid 399 through 401' Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 440 through 452 removed outlier: 3.521A pdb=" N LEU B 445 " --> pdb=" O ASP B 441 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 Processing helix chain 'B' and resid 469 through 474 Processing helix chain 'B' and resid 487 through 497 removed outlier: 3.521A pdb=" N VAL B 497 " --> pdb=" O LEU B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 510 Processing helix chain 'B' and resid 514 through 517 No H-bonds generated for 'chain 'B' and resid 514 through 517' Processing helix chain 'B' and resid 520 through 528 Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 557 through 568 Processing helix chain 'B' and resid 579 through 586 Processing helix chain 'B' and resid 637 through 647 Processing helix chain 'B' and resid 651 through 658 Processing helix chain 'B' and resid 664 through 684 Processing helix chain 'B' and resid 691 through 716 removed outlier: 4.654A pdb=" N ASN B 696 " --> pdb=" O SER B 692 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N HIS B 697 " --> pdb=" O GLN B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 724 Processing helix chain 'B' and resid 730 through 732 No H-bonds generated for 'chain 'B' and resid 730 through 732' Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 750 No H-bonds generated for 'chain 'B' and resid 747 through 750' Processing helix chain 'B' and resid 753 through 763 Processing helix chain 'B' and resid 775 through 782 Processing helix chain 'B' and resid 784 through 787 No H-bonds generated for 'chain 'B' and resid 784 through 787' Processing helix chain 'B' and resid 862 through 868 Processing helix chain 'B' and resid 871 through 894 Processing helix chain 'B' and resid 903 through 924 Processing helix chain 'B' and resid 931 through 940 Processing helix chain 'B' and resid 942 through 961 Processing helix chain 'B' and resid 965 through 992 removed outlier: 4.255A pdb=" N ILE B 980 " --> pdb=" O CYS B 976 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TYR B 981 " --> pdb=" O VAL B 977 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU B 986 " --> pdb=" O TRP B 982 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU B 987 " --> pdb=" O TYR B 983 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASP B 988 " --> pdb=" O ILE B 984 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ILE B 989 " --> pdb=" O ARG B 985 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL B 992 " --> pdb=" O ASP B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 996 through 1032 removed outlier: 4.608A pdb=" N ILE B1008 " --> pdb=" O GLY B1004 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP B1009 " --> pdb=" O LYS B1005 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE B1013 " --> pdb=" O ASP B1009 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE B1016 " --> pdb=" O TYR B1012 " (cutoff:3.500A) Processing helix chain 'B' and resid 1042 through 1045 No H-bonds generated for 'chain 'B' and resid 1042 through 1045' Processing helix chain 'B' and resid 1048 through 1054 removed outlier: 3.984A pdb=" N ILE B1054 " --> pdb=" O PRO B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1088 through 1102 Proline residue: B1092 - end of helix removed outlier: 3.560A pdb=" N ALA B1102 " --> pdb=" O LEU B1099 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1116 Processing helix chain 'B' and resid 1119 through 1142 removed outlier: 4.585A pdb=" N TYR B1134 " --> pdb=" O LYS B1130 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLN B1135 " --> pdb=" O PHE B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1148 through 1150 No H-bonds generated for 'chain 'B' and resid 1148 through 1150' Processing helix chain 'B' and resid 1152 through 1155 No H-bonds generated for 'chain 'B' and resid 1152 through 1155' Processing helix chain 'B' and resid 1157 through 1162 Processing helix chain 'B' and resid 1187 through 1214 Processing helix chain 'B' and resid 1216 through 1239 Processing helix chain 'C' and resid 166 through 175 Processing helix chain 'C' and resid 202 through 214 Processing helix chain 'C' and resid 229 through 241 Processing helix chain 'C' and resid 309 through 321 Processing helix chain 'C' and resid 343 through 354 removed outlier: 4.020A pdb=" N SER C 347 " --> pdb=" O PRO C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 367 No H-bonds generated for 'chain 'C' and resid 365 through 367' Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 398 through 401 Processing helix chain 'C' and resid 408 through 410 No H-bonds generated for 'chain 'C' and resid 408 through 410' Processing helix chain 'C' and resid 414 through 423 removed outlier: 3.962A pdb=" N LYS C 423 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 452 removed outlier: 3.532A pdb=" N LEU C 448 " --> pdb=" O ILE C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 Processing helix chain 'C' and resid 469 through 474 Processing helix chain 'C' and resid 487 through 497 removed outlier: 3.521A pdb=" N VAL C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 510 Processing helix chain 'C' and resid 514 through 517 No H-bonds generated for 'chain 'C' and resid 514 through 517' Processing helix chain 'C' and resid 520 through 528 Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 557 through 568 Processing helix chain 'C' and resid 579 through 586 Processing helix chain 'C' and resid 637 through 647 Processing helix chain 'C' and resid 651 through 658 Processing helix chain 'C' and resid 664 through 684 Processing helix chain 'C' and resid 691 through 716 removed outlier: 3.631A pdb=" N LEU C 695 " --> pdb=" O ILE C 691 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN C 696 " --> pdb=" O SER C 692 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS C 697 " --> pdb=" O GLN C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 718 through 724 Processing helix chain 'C' and resid 730 through 732 No H-bonds generated for 'chain 'C' and resid 730 through 732' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 750 No H-bonds generated for 'chain 'C' and resid 747 through 750' Processing helix chain 'C' and resid 753 through 763 Processing helix chain 'C' and resid 775 through 782 Processing helix chain 'C' and resid 784 through 787 No H-bonds generated for 'chain 'C' and resid 784 through 787' Processing helix chain 'C' and resid 862 through 868 Processing helix chain 'C' and resid 871 through 894 Processing helix chain 'C' and resid 903 through 924 Processing helix chain 'C' and resid 931 through 940 removed outlier: 3.553A pdb=" N GLN C 940 " --> pdb=" O LYS C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 961 Processing helix chain 'C' and resid 965 through 992 removed outlier: 4.275A pdb=" N ILE C 980 " --> pdb=" O CYS C 976 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR C 981 " --> pdb=" O VAL C 977 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU C 986 " --> pdb=" O TRP C 982 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU C 987 " --> pdb=" O TYR C 983 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASP C 988 " --> pdb=" O ILE C 984 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE C 989 " --> pdb=" O ARG C 985 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL C 992 " --> pdb=" O ASP C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1032 removed outlier: 3.770A pdb=" N MET C1007 " --> pdb=" O ILE C1003 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ILE C1008 " --> pdb=" O GLY C1004 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ASP C1009 " --> pdb=" O LYS C1005 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ILE C1016 " --> pdb=" O TYR C1012 " (cutoff:3.500A) Processing helix chain 'C' and resid 1042 through 1045 No H-bonds generated for 'chain 'C' and resid 1042 through 1045' Processing helix chain 'C' and resid 1048 through 1054 removed outlier: 3.988A pdb=" N ILE C1054 " --> pdb=" O PRO C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1060 through 1062 No H-bonds generated for 'chain 'C' and resid 1060 through 1062' Processing helix chain 'C' and resid 1088 through 1102 removed outlier: 3.543A pdb=" N VAL C1091 " --> pdb=" O ALA C1088 " (cutoff:3.500A) Proline residue: C1092 - end of helix removed outlier: 4.144A pdb=" N ALA C1102 " --> pdb=" O LEU C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1107 through 1116 Processing helix chain 'C' and resid 1119 through 1142 removed outlier: 4.597A pdb=" N TYR C1134 " --> pdb=" O LYS C1130 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN C1135 " --> pdb=" O PHE C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1148 through 1150 No H-bonds generated for 'chain 'C' and resid 1148 through 1150' Processing helix chain 'C' and resid 1152 through 1162 removed outlier: 3.687A pdb=" N MET C1158 " --> pdb=" O SER C1154 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE C1159 " --> pdb=" O HIS C1155 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE C1160 " --> pdb=" O MET C1156 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS C1162 " --> pdb=" O MET C1158 " (cutoff:3.500A) Processing helix chain 'C' and resid 1187 through 1214 Processing helix chain 'C' and resid 1216 through 1239 Processing helix chain 'D' and resid 166 through 175 Processing helix chain 'D' and resid 202 through 214 Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 309 through 320 Processing helix chain 'D' and resid 343 through 354 removed outlier: 3.821A pdb=" N SER D 347 " --> pdb=" O PRO D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 414 through 422 removed outlier: 4.729A pdb=" N GLU D 419 " --> pdb=" O ILE D 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 452 removed outlier: 3.556A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 466 Processing helix chain 'D' and resid 469 through 474 Processing helix chain 'D' and resid 487 through 497 removed outlier: 3.519A pdb=" N VAL D 497 " --> pdb=" O LEU D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 510 Processing helix chain 'D' and resid 514 through 517 No H-bonds generated for 'chain 'D' and resid 514 through 517' Processing helix chain 'D' and resid 520 through 528 Processing helix chain 'D' and resid 537 through 544 Processing helix chain 'D' and resid 557 through 568 Processing helix chain 'D' and resid 579 through 586 Processing helix chain 'D' and resid 637 through 647 Processing helix chain 'D' and resid 651 through 658 Processing helix chain 'D' and resid 664 through 684 Processing helix chain 'D' and resid 691 through 716 removed outlier: 4.846A pdb=" N ASN D 696 " --> pdb=" O SER D 692 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N HIS D 697 " --> pdb=" O GLN D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 718 through 724 Processing helix chain 'D' and resid 730 through 732 No H-bonds generated for 'chain 'D' and resid 730 through 732' Processing helix chain 'D' and resid 737 through 743 Processing helix chain 'D' and resid 747 through 750 No H-bonds generated for 'chain 'D' and resid 747 through 750' Processing helix chain 'D' and resid 753 through 763 Processing helix chain 'D' and resid 775 through 782 Processing helix chain 'D' and resid 784 through 786 No H-bonds generated for 'chain 'D' and resid 784 through 786' Processing helix chain 'D' and resid 862 through 868 Processing helix chain 'D' and resid 871 through 894 Processing helix chain 'D' and resid 903 through 924 Processing helix chain 'D' and resid 931 through 938 removed outlier: 3.721A pdb=" N VAL D 935 " --> pdb=" O LEU D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 961 Processing helix chain 'D' and resid 965 through 992 removed outlier: 4.257A pdb=" N ILE D 980 " --> pdb=" O CYS D 976 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR D 981 " --> pdb=" O VAL D 977 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP D 982 " --> pdb=" O ASN D 978 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU D 986 " --> pdb=" O TRP D 982 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU D 987 " --> pdb=" O TYR D 983 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASP D 988 " --> pdb=" O ILE D 984 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE D 989 " --> pdb=" O ARG D 985 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL D 992 " --> pdb=" O ASP D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 996 through 1032 removed outlier: 3.615A pdb=" N VAL D1000 " --> pdb=" O LEU D 996 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ILE D1008 " --> pdb=" O GLY D1004 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASP D1009 " --> pdb=" O LYS D1005 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE D1016 " --> pdb=" O TYR D1012 " (cutoff:3.500A) Processing helix chain 'D' and resid 1048 through 1054 removed outlier: 4.002A pdb=" N ILE D1054 " --> pdb=" O PRO D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1060 through 1062 No H-bonds generated for 'chain 'D' and resid 1060 through 1062' Processing helix chain 'D' and resid 1088 through 1102 Proline residue: D1092 - end of helix removed outlier: 3.577A pdb=" N ALA D1102 " --> pdb=" O LEU D1099 " (cutoff:3.500A) Processing helix chain 'D' and resid 1107 through 1116 Processing helix chain 'D' and resid 1119 through 1142 removed outlier: 4.593A pdb=" N TYR D1134 " --> pdb=" O LYS D1130 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN D1135 " --> pdb=" O PHE D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1148 through 1157 removed outlier: 5.095A pdb=" N ILE D1152 " --> pdb=" O PRO D1149 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE D1153 " --> pdb=" O LEU D1150 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR D1157 " --> pdb=" O SER D1154 " (cutoff:3.500A) Processing helix chain 'D' and resid 1187 through 1214 Processing helix chain 'D' and resid 1216 through 1239 Processing sheet with id= A, first strand: chain 'A' and resid 271 through 275 removed outlier: 8.466A pdb=" N ARG A 272 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR A 143 " --> pdb=" O ARG A 272 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N TYR A 274 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU A 145 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 158 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 271 through 275 removed outlier: 8.480A pdb=" N ARG B 272 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR B 143 " --> pdb=" O ARG B 272 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR B 274 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU B 145 " --> pdb=" O TYR B 274 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 158 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 363 " --> pdb=" O THR B 428 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 271 through 275 removed outlier: 8.501A pdb=" N ARG C 272 " --> pdb=" O PHE C 141 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N THR C 143 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N TYR C 274 " --> pdb=" O THR C 143 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU C 145 " --> pdb=" O TYR C 274 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 158 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL C 363 " --> pdb=" O THR C 428 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 271 through 275 removed outlier: 8.480A pdb=" N ARG D 272 " --> pdb=" O PHE D 141 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR D 143 " --> pdb=" O ARG D 272 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N TYR D 274 " --> pdb=" O THR D 143 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLU D 145 " --> pdb=" O TYR D 274 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL D 158 " --> pdb=" O PHE D 294 " (cutoff:3.500A) 1527 hydrogen bonds defined for protein. 4425 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: 10.58 Time building geometry restraints manager: 12.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9954 1.34 - 1.46: 6682 1.46 - 1.58: 15200 1.58 - 1.69: 0 1.69 - 1.81: 402 Bond restraints: 32238 Sorted by residual: bond pdb=" CA THR D 408 " pdb=" CB THR D 408 " ideal model delta sigma weight residual 1.530 1.548 -0.018 1.69e-02 3.50e+03 1.17e+00 bond pdb=" C PRO D1148 " pdb=" N PRO D1149 " ideal model delta sigma weight residual 1.335 1.347 -0.013 1.19e-02 7.06e+03 1.13e+00 bond pdb=" C GLN D 198 " pdb=" N PRO D 199 " ideal model delta sigma weight residual 1.332 1.344 -0.013 1.26e-02 6.30e+03 9.85e-01 bond pdb=" C TYR A1012 " pdb=" O TYR A1012 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.15e-02 7.56e+03 8.62e-01 bond pdb=" C PRO C1148 " pdb=" N PRO C1149 " ideal model delta sigma weight residual 1.335 1.346 -0.012 1.28e-02 6.10e+03 8.42e-01 ... (remaining 32233 not shown) Histogram of bond angle deviations from ideal: 99.63 - 106.54: 936 106.54 - 113.44: 17847 113.44 - 120.35: 12348 120.35 - 127.26: 12091 127.26 - 134.17: 381 Bond angle restraints: 43603 Sorted by residual: angle pdb=" C VAL A 688 " pdb=" N ASP A 689 " pdb=" CA ASP A 689 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C VAL B 688 " pdb=" N ASP B 689 " pdb=" CA ASP B 689 " ideal model delta sigma weight residual 121.54 127.83 -6.29 1.91e+00 2.74e-01 1.09e+01 angle pdb=" N PRO B1148 " pdb=" CA PRO B1148 " pdb=" C PRO B1148 " ideal model delta sigma weight residual 110.70 114.68 -3.98 1.22e+00 6.72e-01 1.06e+01 angle pdb=" N PRO A1148 " pdb=" CA PRO A1148 " pdb=" C PRO A1148 " ideal model delta sigma weight residual 110.70 114.51 -3.81 1.22e+00 6.72e-01 9.74e+00 angle pdb=" N PRO C1148 " pdb=" CA PRO C1148 " pdb=" C PRO C1148 " ideal model delta sigma weight residual 110.70 114.46 -3.76 1.22e+00 6.72e-01 9.49e+00 ... (remaining 43598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 17708 15.42 - 30.83: 1360 30.83 - 46.25: 366 46.25 - 61.66: 99 61.66 - 77.08: 4 Dihedral angle restraints: 19537 sinusoidal: 8187 harmonic: 11350 Sorted by residual: dihedral pdb=" CA THR D 356 " pdb=" C THR D 356 " pdb=" N PRO D 357 " pdb=" CA PRO D 357 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA THR C 356 " pdb=" C THR C 356 " pdb=" N PRO C 357 " pdb=" CA PRO C 357 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA THR A 356 " pdb=" C THR A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta harmonic sigma weight residual 180.00 159.20 20.80 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 19534 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2991 0.032 - 0.065: 1440 0.065 - 0.097: 314 0.097 - 0.129: 142 0.129 - 0.162: 10 Chirality restraints: 4897 Sorted by residual: chirality pdb=" C08 9Z9 A1402 " pdb=" C07 9Z9 A1402 " pdb=" C09 9Z9 A1402 " pdb=" C11 9Z9 A1402 " both_signs ideal model delta sigma weight residual False 2.45 2.62 -0.16 2.00e-01 2.50e+01 6.53e-01 chirality pdb=" C08 9Z9 B1401 " pdb=" C07 9Z9 B1401 " pdb=" C09 9Z9 B1401 " pdb=" C11 9Z9 B1401 " both_signs ideal model delta sigma weight residual False 2.45 2.61 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" C08 9Z9 A1401 " pdb=" C07 9Z9 A1401 " pdb=" C09 9Z9 A1401 " pdb=" C11 9Z9 A1401 " both_signs ideal model delta sigma weight residual False 2.45 2.61 -0.16 2.00e-01 2.50e+01 6.21e-01 ... (remaining 4894 not shown) Planarity restraints: 5416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 784 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO A 785 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 785 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 785 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 784 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.19e+00 pdb=" N PRO C 785 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 785 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 785 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 784 " -0.038 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO D 785 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 785 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 785 " -0.032 5.00e-02 4.00e+02 ... (remaining 5413 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 5489 2.76 - 3.30: 31212 3.30 - 3.83: 51043 3.83 - 4.37: 57460 4.37 - 4.90: 101231 Nonbonded interactions: 246435 Sorted by model distance: nonbonded pdb=" O HIS A 240 " pdb=" OG SER A 244 " model vdw 2.230 2.440 nonbonded pdb=" O GLU C 922 " pdb=" OG SER C 926 " model vdw 2.248 2.440 nonbonded pdb=" O ILE C 399 " pdb=" OG1 THR C 402 " model vdw 2.276 2.440 nonbonded pdb=" OD1 ASP D 947 " pdb=" OH TYR D 981 " model vdw 2.286 2.440 nonbonded pdb=" OD1 ASP A 947 " pdb=" OH TYR A 981 " model vdw 2.291 2.440 ... (remaining 246430 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 129 through 1059 or resid 1085 through 1243)) selection = (chain 'B' and (resid 129 through 1059 or resid 1085 through 1243)) selection = (chain 'C' and (resid 129 through 1059 or resid 1085 through 1243)) selection = (chain 'D' and (resid 129 through 1059 or resid 1085 through 1243)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.650 Check model and map are aligned: 0.470 Set scattering table: 0.330 Process input model: 80.960 Find NCS groups from input model: 2.860 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 0.004 0.035 32238 Z= 0.227 Angle : 0.541 8.860 43603 Z= 0.288 Chirality : 0.040 0.162 4897 Planarity : 0.004 0.057 5416 Dihedral : 12.282 77.077 12197 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.92 % Allowed : 8.26 % Favored : 88.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.14), residues: 3770 helix: 1.26 (0.11), residues: 2343 sheet: 0.03 (0.37), residues: 222 loop : -1.29 (0.17), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 763 HIS 0.003 0.001 HIS C 240 PHE 0.011 0.001 PHE B 792 TYR 0.010 0.001 TYR A1048 ARG 0.004 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 483 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 ILE cc_start: 0.5895 (OUTLIER) cc_final: 0.5352 (mm) REVERT: A 479 TYR cc_start: 0.5170 (OUTLIER) cc_final: 0.3868 (m-80) REVERT: A 665 MET cc_start: 0.7824 (mtm) cc_final: 0.7423 (mtm) REVERT: A 669 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8812 (mm) REVERT: A 772 ASN cc_start: 0.8448 (t0) cc_final: 0.8221 (p0) REVERT: A 778 ILE cc_start: 0.9286 (pt) cc_final: 0.9009 (mt) REVERT: A 924 LEU cc_start: 0.8889 (pp) cc_final: 0.8653 (mt) REVERT: A 925 MET cc_start: 0.7778 (ppp) cc_final: 0.7475 (ppp) REVERT: A 932 LEU cc_start: 0.9255 (tt) cc_final: 0.8951 (mm) REVERT: A 1010 MET cc_start: 0.7232 (tmm) cc_final: 0.6821 (tmm) REVERT: A 1022 MET cc_start: 0.7398 (mtm) cc_final: 0.7154 (mtp) REVERT: A 1049 MET cc_start: 0.6665 (mpp) cc_final: 0.6369 (mpp) REVERT: A 1051 TYR cc_start: 0.8073 (t80) cc_final: 0.6875 (t80) REVERT: A 1055 TYR cc_start: 0.7025 (m-10) cc_final: 0.6342 (m-10) REVERT: A 1103 ASN cc_start: 0.7606 (m-40) cc_final: 0.7147 (m110) REVERT: A 1230 MET cc_start: 0.8487 (ttm) cc_final: 0.8008 (ttm) REVERT: B 409 GLN cc_start: 0.6454 (tp40) cc_final: 0.6074 (mm-40) REVERT: B 412 HIS cc_start: 0.3239 (OUTLIER) cc_final: 0.1783 (m-70) REVERT: B 665 MET cc_start: 0.7784 (mtm) cc_final: 0.7394 (mtm) REVERT: B 669 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8772 (mm) REVERT: B 764 MET cc_start: 0.8991 (mmt) cc_final: 0.8725 (mmt) REVERT: B 925 MET cc_start: 0.7509 (ppp) cc_final: 0.7242 (ppp) REVERT: B 948 LEU cc_start: 0.8711 (mt) cc_final: 0.8488 (mt) REVERT: B 958 MET cc_start: 0.6122 (mmm) cc_final: 0.5921 (tmm) REVERT: B 1022 MET cc_start: 0.7154 (mtp) cc_final: 0.6653 (mtm) REVERT: B 1053 MET cc_start: 0.7942 (mtt) cc_final: 0.7618 (mtt) REVERT: B 1095 MET cc_start: 0.7501 (tpp) cc_final: 0.7239 (tpp) REVERT: B 1100 LEU cc_start: 0.9134 (tp) cc_final: 0.8924 (tt) REVERT: B 1230 MET cc_start: 0.8456 (ttm) cc_final: 0.7911 (ttm) REVERT: C 266 ILE cc_start: 0.5838 (OUTLIER) cc_final: 0.5289 (mm) REVERT: C 633 HIS cc_start: 0.6296 (m90) cc_final: 0.6058 (m90) REVERT: C 665 MET cc_start: 0.7745 (mtm) cc_final: 0.7367 (mtm) REVERT: C 669 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8764 (mm) REVERT: C 726 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.9011 (m) REVERT: C 769 MET cc_start: 0.7922 (ttm) cc_final: 0.7677 (ttp) REVERT: C 772 ASN cc_start: 0.8778 (t0) cc_final: 0.8491 (p0) REVERT: C 778 ILE cc_start: 0.9143 (pt) cc_final: 0.8870 (mt) REVERT: C 958 MET cc_start: 0.6526 (mmm) cc_final: 0.6258 (tmm) REVERT: C 1053 MET cc_start: 0.7945 (mtt) cc_final: 0.7624 (mtt) REVERT: C 1058 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7902 (p) REVERT: C 1095 MET cc_start: 0.7382 (tpp) cc_final: 0.7102 (tpp) REVERT: C 1230 MET cc_start: 0.8402 (ttm) cc_final: 0.7939 (ttp) REVERT: D 240 HIS cc_start: 0.7572 (t-90) cc_final: 0.7318 (t70) REVERT: D 266 ILE cc_start: 0.5843 (OUTLIER) cc_final: 0.5302 (mm) REVERT: D 411 GLN cc_start: 0.5565 (OUTLIER) cc_final: 0.5302 (tp-100) REVERT: D 665 MET cc_start: 0.7745 (mtm) cc_final: 0.7363 (mtm) REVERT: D 669 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8779 (mm) REVERT: D 764 MET cc_start: 0.9091 (mmt) cc_final: 0.8711 (mmt) REVERT: D 778 ILE cc_start: 0.9177 (pt) cc_final: 0.8874 (mt) REVERT: D 924 LEU cc_start: 0.8752 (pp) cc_final: 0.8383 (mp) REVERT: D 930 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8269 (tptt) REVERT: D 958 MET cc_start: 0.6797 (mmm) cc_final: 0.6595 (mmm) REVERT: D 1010 MET cc_start: 0.7222 (tmm) cc_final: 0.6867 (tmm) REVERT: D 1022 MET cc_start: 0.7308 (mtm) cc_final: 0.7082 (mtp) REVERT: D 1051 TYR cc_start: 0.8055 (t80) cc_final: 0.7831 (t80) REVERT: D 1053 MET cc_start: 0.7875 (mtt) cc_final: 0.7644 (mtt) REVERT: D 1055 TYR cc_start: 0.7236 (m-80) cc_final: 0.7032 (m-10) REVERT: D 1058 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.7916 (p) REVERT: D 1095 MET cc_start: 0.7637 (tpp) cc_final: 0.7288 (tpp) REVERT: D 1099 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8597 (mp) REVERT: D 1103 ASN cc_start: 0.7419 (m-40) cc_final: 0.7111 (m110) outliers start: 99 outliers final: 45 residues processed: 560 average time/residue: 0.4318 time to fit residues: 385.5820 Evaluate side-chains 431 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 371 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 327 ARG Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 726 THR Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1009 ASP Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1058 VAL Chi-restraints excluded: chain C residue 1155 HIS Chi-restraints excluded: chain C residue 1186 THR Chi-restraints excluded: chain D residue 266 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 411 GLN Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1099 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.6980 chunk 291 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 155 optimal weight: 2.9990 chunk 300 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 348 optimal weight: 8.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 275 GLN A 279 ASN A 575 ASN A 772 ASN A 965 GLN A1115 ASN A1161 GLN B 275 GLN B 279 ASN B 575 ASN ** B 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN B1115 ASN B1161 GLN C 275 GLN C 279 ASN C 531 HIS C 575 ASN C 719 GLN C 772 ASN C 965 GLN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN C1161 GLN D 275 GLN D 279 ASN D 409 GLN D 575 ASN D 719 GLN D 965 GLN ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN D1161 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 32238 Z= 0.425 Angle : 0.661 10.507 43603 Z= 0.334 Chirality : 0.043 0.195 4897 Planarity : 0.005 0.056 5416 Dihedral : 7.871 65.716 4688 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.92 % Allowed : 12.89 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.57 (0.14), residues: 3770 helix: 1.29 (0.11), residues: 2355 sheet: -0.40 (0.35), residues: 231 loop : -1.29 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 763 HIS 0.005 0.001 HIS A 318 PHE 0.020 0.002 PHE C1140 TYR 0.011 0.002 TYR B 981 ARG 0.006 0.001 ARG D 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 380 time to evaluate : 4.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 479 TYR cc_start: 0.5201 (OUTLIER) cc_final: 0.3952 (m-80) REVERT: A 665 MET cc_start: 0.7869 (mtm) cc_final: 0.7537 (mtm) REVERT: A 669 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8764 (mm) REVERT: A 788 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7411 (pp) REVERT: A 925 MET cc_start: 0.7812 (ppp) cc_final: 0.7466 (ppp) REVERT: A 1010 MET cc_start: 0.7542 (tmm) cc_final: 0.7284 (tmm) REVERT: A 1051 TYR cc_start: 0.8157 (t80) cc_final: 0.6876 (t80) REVERT: A 1055 TYR cc_start: 0.7065 (m-10) cc_final: 0.6305 (m-10) REVERT: A 1230 MET cc_start: 0.8628 (ttm) cc_final: 0.8364 (ttm) REVERT: B 266 ILE cc_start: 0.5946 (OUTLIER) cc_final: 0.5364 (mm) REVERT: B 412 HIS cc_start: 0.3183 (OUTLIER) cc_final: 0.2251 (m-70) REVERT: B 665 MET cc_start: 0.7842 (mtm) cc_final: 0.7511 (mtm) REVERT: B 669 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8738 (mm) REVERT: B 788 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7805 (pp) REVERT: B 925 MET cc_start: 0.7544 (ppp) cc_final: 0.7281 (ppp) REVERT: B 958 MET cc_start: 0.6359 (mmm) cc_final: 0.6152 (tmm) REVERT: B 1053 MET cc_start: 0.7971 (mtt) cc_final: 0.7657 (mtt) REVERT: B 1055 TYR cc_start: 0.7086 (m-10) cc_final: 0.6792 (m-10) REVERT: B 1095 MET cc_start: 0.7698 (tpp) cc_final: 0.7401 (tpp) REVERT: B 1230 MET cc_start: 0.8688 (ttm) cc_final: 0.8436 (ttm) REVERT: C 418 MET cc_start: 0.8852 (tpp) cc_final: 0.7388 (tmm) REVERT: C 432 MET cc_start: 0.6231 (OUTLIER) cc_final: 0.5923 (mtt) REVERT: C 479 TYR cc_start: 0.5441 (OUTLIER) cc_final: 0.3976 (m-80) REVERT: C 633 HIS cc_start: 0.6333 (m90) cc_final: 0.6119 (m90) REVERT: C 665 MET cc_start: 0.7801 (mtm) cc_final: 0.7468 (mtm) REVERT: C 669 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8733 (mm) REVERT: C 788 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7575 (pp) REVERT: C 958 MET cc_start: 0.6822 (mmm) cc_final: 0.6595 (tmm) REVERT: C 1051 TYR cc_start: 0.8281 (t80) cc_final: 0.8006 (t80) REVERT: C 1053 MET cc_start: 0.8043 (mtt) cc_final: 0.7823 (mtm) REVERT: C 1095 MET cc_start: 0.7744 (tpp) cc_final: 0.7463 (tpp) REVERT: C 1230 MET cc_start: 0.8663 (ttm) cc_final: 0.8243 (ttm) REVERT: D 665 MET cc_start: 0.7823 (mtm) cc_final: 0.7496 (mtm) REVERT: D 669 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8751 (mm) REVERT: D 778 ILE cc_start: 0.9169 (pt) cc_final: 0.8924 (mt) REVERT: D 788 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7434 (pp) REVERT: D 930 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8281 (tptt) REVERT: D 958 MET cc_start: 0.6995 (mmm) cc_final: 0.6695 (mmm) REVERT: D 1010 MET cc_start: 0.7200 (tmm) cc_final: 0.6984 (tmm) REVERT: D 1051 TYR cc_start: 0.8272 (t80) cc_final: 0.8065 (t80) REVERT: D 1058 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7848 (p) REVERT: D 1095 MET cc_start: 0.7842 (tpp) cc_final: 0.7467 (tpp) REVERT: D 1099 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8482 (mp) REVERT: D 1103 ASN cc_start: 0.7328 (m-40) cc_final: 0.7077 (m110) REVERT: D 1150 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8287 (mp) outliers start: 133 outliers final: 57 residues processed: 484 average time/residue: 0.3850 time to fit residues: 309.0177 Evaluate side-chains 436 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 362 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 956 VAL Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 432 MET Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1009 ASP Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1186 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 930 LYS Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 932 LEU Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1009 ASP Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1058 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1150 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 290 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 349 optimal weight: 0.9980 chunk 377 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 chunk 346 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 280 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 GLN A1116 ASN B 531 HIS B1115 ASN B1155 HIS ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 32238 Z= 0.304 Angle : 0.571 8.421 43603 Z= 0.288 Chirality : 0.040 0.173 4897 Planarity : 0.004 0.058 5416 Dihedral : 7.615 75.150 4663 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.69 % Allowed : 15.39 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.14), residues: 3770 helix: 1.46 (0.11), residues: 2351 sheet: -0.44 (0.34), residues: 231 loop : -1.24 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 763 HIS 0.008 0.001 HIS B 151 PHE 0.016 0.001 PHE A 954 TYR 0.010 0.001 TYR D1048 ARG 0.007 0.000 ARG C1143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 375 time to evaluate : 3.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.7363 (OUTLIER) cc_final: 0.7109 (m-10) REVERT: A 479 TYR cc_start: 0.5064 (OUTLIER) cc_final: 0.3876 (m-80) REVERT: A 665 MET cc_start: 0.7808 (mtm) cc_final: 0.7473 (mtm) REVERT: A 669 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8834 (mm) REVERT: A 788 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7373 (pp) REVERT: A 1010 MET cc_start: 0.7407 (tmm) cc_final: 0.7154 (tmm) REVERT: A 1051 TYR cc_start: 0.8134 (t80) cc_final: 0.6942 (t80) REVERT: A 1055 TYR cc_start: 0.7100 (m-10) cc_final: 0.6369 (m-10) REVERT: A 1230 MET cc_start: 0.8593 (ttm) cc_final: 0.8377 (ttm) REVERT: B 412 HIS cc_start: 0.3434 (OUTLIER) cc_final: 0.2286 (m-70) REVERT: B 418 MET cc_start: 0.8531 (tpt) cc_final: 0.8259 (tpt) REVERT: B 479 TYR cc_start: 0.5285 (OUTLIER) cc_final: 0.3576 (m-80) REVERT: B 665 MET cc_start: 0.7788 (mtm) cc_final: 0.7454 (mtm) REVERT: B 669 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8811 (mm) REVERT: B 788 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7774 (pp) REVERT: B 917 ILE cc_start: 0.8503 (pt) cc_final: 0.8160 (mt) REVERT: B 925 MET cc_start: 0.7640 (ppp) cc_final: 0.7327 (ppp) REVERT: B 1051 TYR cc_start: 0.8122 (t80) cc_final: 0.6987 (t80) REVERT: B 1053 MET cc_start: 0.7977 (mtt) cc_final: 0.7751 (mtt) REVERT: B 1055 TYR cc_start: 0.7081 (m-10) cc_final: 0.6796 (m-10) REVERT: B 1059 PHE cc_start: 0.6921 (m-10) cc_final: 0.6721 (m-10) REVERT: B 1230 MET cc_start: 0.8622 (ttm) cc_final: 0.8372 (ttm) REVERT: C 418 MET cc_start: 0.8829 (tpp) cc_final: 0.7347 (tmm) REVERT: C 479 TYR cc_start: 0.5405 (OUTLIER) cc_final: 0.3949 (m-80) REVERT: C 665 MET cc_start: 0.7747 (mtm) cc_final: 0.7414 (mtm) REVERT: C 669 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8814 (mm) REVERT: C 788 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7565 (pp) REVERT: C 958 MET cc_start: 0.6681 (mmm) cc_final: 0.6456 (tmm) REVERT: C 1051 TYR cc_start: 0.8270 (t80) cc_final: 0.7921 (t80) REVERT: C 1053 MET cc_start: 0.8006 (mtt) cc_final: 0.7785 (mtt) REVERT: C 1095 MET cc_start: 0.7657 (tpp) cc_final: 0.7377 (tpp) REVERT: C 1103 ASN cc_start: 0.7399 (m-40) cc_final: 0.7073 (m-40) REVERT: C 1230 MET cc_start: 0.8559 (ttm) cc_final: 0.8141 (ttm) REVERT: D 665 MET cc_start: 0.7769 (mtm) cc_final: 0.7439 (mtm) REVERT: D 669 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8821 (mm) REVERT: D 778 ILE cc_start: 0.9175 (pt) cc_final: 0.8909 (mt) REVERT: D 788 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7313 (pp) REVERT: D 958 MET cc_start: 0.6895 (mmm) cc_final: 0.6645 (mmm) REVERT: D 1010 MET cc_start: 0.7221 (tmm) cc_final: 0.6974 (tmm) REVERT: D 1051 TYR cc_start: 0.8264 (t80) cc_final: 0.8038 (t80) REVERT: D 1095 MET cc_start: 0.7950 (tpp) cc_final: 0.7664 (tpp) outliers start: 125 outliers final: 74 residues processed: 471 average time/residue: 0.3856 time to fit residues: 303.4060 Evaluate side-chains 444 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 357 time to evaluate : 4.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1104 ILE Chi-restraints excluded: chain B residue 1155 HIS Chi-restraints excluded: chain B residue 1178 ASP Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1003 ILE Chi-restraints excluded: chain C residue 1009 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1155 HIS Chi-restraints excluded: chain C residue 1186 THR Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 932 LEU Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1009 ASP Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 234 optimal weight: 1.9990 chunk 350 optimal weight: 0.9980 chunk 371 optimal weight: 1.9990 chunk 183 optimal weight: 0.0980 chunk 332 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 HIS A1115 ASN B 291 HIS ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN D 531 HIS ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1155 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 32238 Z= 0.219 Angle : 0.541 10.161 43603 Z= 0.268 Chirality : 0.039 0.166 4897 Planarity : 0.004 0.057 5416 Dihedral : 7.386 70.304 4652 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.89 % Allowed : 15.69 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.14), residues: 3770 helix: 1.68 (0.11), residues: 2349 sheet: -0.43 (0.34), residues: 231 loop : -1.18 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 763 HIS 0.014 0.001 HIS B1155 PHE 0.022 0.001 PHE A1047 TYR 0.010 0.001 TYR D1048 ARG 0.004 0.000 ARG B 407 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 371 time to evaluate : 5.004 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: A 352 TYR cc_start: 0.7360 (OUTLIER) cc_final: 0.7069 (m-10) REVERT: A 479 TYR cc_start: 0.5015 (OUTLIER) cc_final: 0.3857 (m-80) REVERT: A 665 MET cc_start: 0.7753 (mtm) cc_final: 0.7422 (mtm) REVERT: A 669 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8805 (mm) REVERT: A 788 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7379 (pp) REVERT: A 948 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8505 (mt) REVERT: A 985 ARG cc_start: 0.8361 (tmm-80) cc_final: 0.7906 (ttm-80) REVERT: A 1010 MET cc_start: 0.7374 (tmm) cc_final: 0.7122 (tmm) REVERT: A 1051 TYR cc_start: 0.8162 (t80) cc_final: 0.6814 (t80) REVERT: A 1055 TYR cc_start: 0.7123 (m-10) cc_final: 0.6423 (m-80) REVERT: B 266 ILE cc_start: 0.5937 (OUTLIER) cc_final: 0.5399 (mm) REVERT: B 412 HIS cc_start: 0.3136 (OUTLIER) cc_final: 0.2073 (m-70) REVERT: B 418 MET cc_start: 0.8514 (tpt) cc_final: 0.8147 (tpt) REVERT: B 479 TYR cc_start: 0.5239 (OUTLIER) cc_final: 0.3573 (m-80) REVERT: B 665 MET cc_start: 0.7739 (mtm) cc_final: 0.7409 (mtm) REVERT: B 669 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8791 (mm) REVERT: B 788 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7758 (pp) REVERT: B 925 MET cc_start: 0.7608 (ppp) cc_final: 0.7301 (ppp) REVERT: B 1053 MET cc_start: 0.7975 (mtt) cc_final: 0.7735 (mtt) REVERT: B 1055 TYR cc_start: 0.7063 (m-10) cc_final: 0.6784 (m-10) REVERT: B 1230 MET cc_start: 0.8537 (ttm) cc_final: 0.8267 (ttm) REVERT: C 418 MET cc_start: 0.8841 (tpp) cc_final: 0.7390 (tmm) REVERT: C 479 TYR cc_start: 0.5217 (OUTLIER) cc_final: 0.3775 (m-80) REVERT: C 665 MET cc_start: 0.7697 (mtm) cc_final: 0.7368 (mtm) REVERT: C 669 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8788 (mm) REVERT: C 769 MET cc_start: 0.7990 (ttp) cc_final: 0.7732 (tmm) REVERT: C 788 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7552 (pp) REVERT: C 958 MET cc_start: 0.6688 (mmm) cc_final: 0.6386 (tmm) REVERT: C 1051 TYR cc_start: 0.8228 (t80) cc_final: 0.7923 (t80) REVERT: C 1053 MET cc_start: 0.7931 (mtt) cc_final: 0.7658 (mtt) REVERT: C 1103 ASN cc_start: 0.7376 (m-40) cc_final: 0.7131 (m-40) REVERT: C 1230 MET cc_start: 0.8537 (ttm) cc_final: 0.8129 (ttm) REVERT: D 479 TYR cc_start: 0.5131 (OUTLIER) cc_final: 0.3864 (m-80) REVERT: D 665 MET cc_start: 0.7714 (mtm) cc_final: 0.7385 (mtm) REVERT: D 669 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8797 (mm) REVERT: D 778 ILE cc_start: 0.9163 (pt) cc_final: 0.8889 (mt) REVERT: D 788 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7373 (pp) REVERT: D 941 GLU cc_start: 0.7820 (mp0) cc_final: 0.7576 (tp30) REVERT: D 958 MET cc_start: 0.6824 (mmm) cc_final: 0.6572 (mmm) REVERT: D 1010 MET cc_start: 0.7264 (tmm) cc_final: 0.7013 (tmm) REVERT: D 1051 TYR cc_start: 0.8238 (t80) cc_final: 0.7978 (t80) REVERT: D 1150 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8305 (mp) outliers start: 132 outliers final: 83 residues processed: 474 average time/residue: 0.3831 time to fit residues: 302.5733 Evaluate side-chains 462 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 362 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 983 TYR Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1242 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1003 ILE Chi-restraints excluded: chain C residue 1009 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain C residue 1155 HIS Chi-restraints excluded: chain C residue 1186 THR Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 414 PHE Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 985 ARG Chi-restraints excluded: chain D residue 1009 ASP Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1150 LEU Chi-restraints excluded: chain D residue 1155 HIS Chi-restraints excluded: chain D residue 1242 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.0020 chunk 210 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 276 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 316 optimal weight: 5.9990 chunk 256 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.6980 chunk 333 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 0.7468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1115 ASN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32238 Z= 0.164 Angle : 0.517 9.630 43603 Z= 0.255 Chirality : 0.038 0.170 4897 Planarity : 0.004 0.053 5416 Dihedral : 7.243 65.012 4651 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.89 % Allowed : 16.31 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.21 (0.14), residues: 3770 helix: 1.87 (0.11), residues: 2349 sheet: -0.33 (0.34), residues: 231 loop : -1.15 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 763 HIS 0.023 0.001 HIS D1155 PHE 0.020 0.001 PHE B1047 TYR 0.013 0.001 TYR D 865 ARG 0.004 0.000 ARG B 985 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 370 time to evaluate : 3.699 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: A 352 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.7033 (m-10) REVERT: A 479 TYR cc_start: 0.5263 (OUTLIER) cc_final: 0.4145 (m-80) REVERT: A 665 MET cc_start: 0.7648 (mtm) cc_final: 0.7301 (mtm) REVERT: A 669 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8775 (mm) REVERT: A 788 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7309 (pp) REVERT: A 948 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8376 (mt) REVERT: A 985 ARG cc_start: 0.8312 (tmm-80) cc_final: 0.7911 (ttm-80) REVERT: A 1010 MET cc_start: 0.7332 (tmm) cc_final: 0.7074 (tmm) REVERT: A 1051 TYR cc_start: 0.8015 (t80) cc_final: 0.6826 (t80) REVERT: A 1055 TYR cc_start: 0.7152 (m-10) cc_final: 0.6665 (m-80) REVERT: A 1138 MET cc_start: 0.8358 (mmt) cc_final: 0.8142 (mpp) REVERT: B 266 ILE cc_start: 0.5968 (OUTLIER) cc_final: 0.5464 (mm) REVERT: B 412 HIS cc_start: 0.3318 (OUTLIER) cc_final: 0.2219 (m-70) REVERT: B 418 MET cc_start: 0.8436 (tpt) cc_final: 0.8073 (tpt) REVERT: B 479 TYR cc_start: 0.5123 (OUTLIER) cc_final: 0.3471 (m-80) REVERT: B 665 MET cc_start: 0.7718 (mtm) cc_final: 0.7403 (mtm) REVERT: B 669 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8791 (mm) REVERT: B 925 MET cc_start: 0.7636 (ppp) cc_final: 0.7342 (ppp) REVERT: B 1230 MET cc_start: 0.8536 (ttm) cc_final: 0.8328 (ttm) REVERT: C 479 TYR cc_start: 0.5160 (OUTLIER) cc_final: 0.3726 (m-80) REVERT: C 642 MET cc_start: 0.8593 (tpp) cc_final: 0.8362 (tpp) REVERT: C 665 MET cc_start: 0.7604 (mtm) cc_final: 0.7268 (mtm) REVERT: C 669 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8766 (mm) REVERT: C 769 MET cc_start: 0.7961 (ttp) cc_final: 0.7757 (tmm) REVERT: C 788 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7569 (pp) REVERT: C 958 MET cc_start: 0.6588 (mmm) cc_final: 0.6335 (tmm) REVERT: C 1053 MET cc_start: 0.7920 (mtt) cc_final: 0.7682 (mtt) REVERT: C 1230 MET cc_start: 0.8488 (ttm) cc_final: 0.8040 (ttm) REVERT: D 479 TYR cc_start: 0.5032 (OUTLIER) cc_final: 0.3793 (m-80) REVERT: D 665 MET cc_start: 0.7697 (mtm) cc_final: 0.7374 (mtm) REVERT: D 669 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8769 (mm) REVERT: D 775 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7224 (pp) REVERT: D 778 ILE cc_start: 0.9143 (pt) cc_final: 0.8867 (mt) REVERT: D 788 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7308 (pp) REVERT: D 1010 MET cc_start: 0.7361 (tmm) cc_final: 0.6928 (tmm) outliers start: 132 outliers final: 77 residues processed: 465 average time/residue: 0.4154 time to fit residues: 320.5473 Evaluate side-chains 454 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 361 time to evaluate : 3.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain A residue 1242 HIS Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1048 TYR Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1178 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1003 ILE Chi-restraints excluded: chain C residue 1009 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 775 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 985 ARG Chi-restraints excluded: chain D residue 1009 ASP Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1242 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 6.9990 chunk 334 optimal weight: 0.0040 chunk 73 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 371 optimal weight: 0.9980 chunk 308 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 195 optimal weight: 0.7980 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 ASN ** D 772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1155 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32238 Z= 0.216 Angle : 0.548 15.034 43603 Z= 0.267 Chirality : 0.038 0.171 4897 Planarity : 0.004 0.056 5416 Dihedral : 7.157 64.428 4643 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.25 % Allowed : 16.19 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.14), residues: 3770 helix: 1.90 (0.11), residues: 2343 sheet: -0.35 (0.33), residues: 231 loop : -1.07 (0.18), residues: 1196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 763 HIS 0.003 0.001 HIS C 189 PHE 0.029 0.001 PHE D1024 TYR 0.013 0.001 TYR C 865 ARG 0.004 0.000 ARG D1143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 367 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.7373 (OUTLIER) cc_final: 0.7084 (m-10) REVERT: A 479 TYR cc_start: 0.5503 (OUTLIER) cc_final: 0.4362 (m-80) REVERT: A 665 MET cc_start: 0.7794 (mtm) cc_final: 0.7475 (mtm) REVERT: A 669 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8832 (mm) REVERT: A 788 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7307 (pp) REVERT: A 932 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8811 (mm) REVERT: A 948 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8455 (mt) REVERT: A 985 ARG cc_start: 0.8332 (tmm-80) cc_final: 0.7713 (ttm-80) REVERT: A 1010 MET cc_start: 0.7511 (tmm) cc_final: 0.7247 (tmm) REVERT: A 1051 TYR cc_start: 0.8047 (t80) cc_final: 0.6712 (t80) REVERT: A 1055 TYR cc_start: 0.7116 (m-10) cc_final: 0.6418 (m-80) REVERT: A 1138 MET cc_start: 0.8360 (mmt) cc_final: 0.8130 (mpp) REVERT: B 266 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5487 (mm) REVERT: B 412 HIS cc_start: 0.3220 (OUTLIER) cc_final: 0.1953 (m-70) REVERT: B 418 MET cc_start: 0.8520 (tpt) cc_final: 0.8185 (tpt) REVERT: B 479 TYR cc_start: 0.5231 (OUTLIER) cc_final: 0.3581 (m-80) REVERT: B 665 MET cc_start: 0.7778 (mtm) cc_final: 0.7458 (mtm) REVERT: B 669 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8809 (mm) REVERT: B 788 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7685 (pp) REVERT: B 925 MET cc_start: 0.7681 (ppp) cc_final: 0.7413 (ppp) REVERT: B 1055 TYR cc_start: 0.7116 (m-10) cc_final: 0.6826 (m-10) REVERT: C 420 CYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7888 (t) REVERT: C 479 TYR cc_start: 0.5242 (OUTLIER) cc_final: 0.3805 (m-80) REVERT: C 665 MET cc_start: 0.7742 (mtm) cc_final: 0.7424 (mtm) REVERT: C 669 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8811 (mm) REVERT: C 788 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7586 (pp) REVERT: C 1230 MET cc_start: 0.8503 (ttm) cc_final: 0.8078 (ttm) REVERT: D 479 TYR cc_start: 0.5075 (OUTLIER) cc_final: 0.3863 (m-80) REVERT: D 665 MET cc_start: 0.7760 (mtm) cc_final: 0.7444 (mtm) REVERT: D 669 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8814 (mm) REVERT: D 778 ILE cc_start: 0.9153 (pt) cc_final: 0.8870 (mt) REVERT: D 788 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7324 (pp) REVERT: D 1010 MET cc_start: 0.7533 (tmm) cc_final: 0.7081 (tmm) REVERT: D 1150 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8273 (mp) outliers start: 144 outliers final: 87 residues processed: 474 average time/residue: 0.3737 time to fit residues: 297.4075 Evaluate side-chains 466 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 360 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1242 HIS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 956 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1009 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 MET Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain C residue 1155 HIS Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 956 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1009 ASP Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1048 TYR Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1150 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1155 HIS Chi-restraints excluded: chain D residue 1242 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 211 optimal weight: 6.9990 chunk 271 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 chunk 312 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 370 optimal weight: 0.5980 chunk 231 optimal weight: 3.9990 chunk 225 optimal weight: 4.9990 chunk 170 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1115 ASN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1115 ASN C1126 ASN ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1155 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32238 Z= 0.283 Angle : 0.598 14.076 43603 Z= 0.294 Chirality : 0.040 0.160 4897 Planarity : 0.004 0.057 5416 Dihedral : 7.174 67.265 4638 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.36 % Allowed : 16.10 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.16 (0.14), residues: 3770 helix: 1.80 (0.11), residues: 2349 sheet: -0.42 (0.33), residues: 231 loop : -1.08 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 763 HIS 0.010 0.001 HIS D1155 PHE 0.022 0.001 PHE B1047 TYR 0.014 0.001 TYR D 865 ARG 0.011 0.000 ARG D 985 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 364 time to evaluate : 3.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.7510 (OUTLIER) cc_final: 0.7254 (m-10) REVERT: A 479 TYR cc_start: 0.5546 (OUTLIER) cc_final: 0.4408 (m-80) REVERT: A 665 MET cc_start: 0.7804 (mtm) cc_final: 0.7472 (mtm) REVERT: A 669 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8748 (mm) REVERT: A 788 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7296 (pp) REVERT: A 932 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8823 (mm) REVERT: A 948 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8454 (mt) REVERT: A 985 ARG cc_start: 0.8360 (tmm-80) cc_final: 0.7704 (ttm-80) REVERT: A 1010 MET cc_start: 0.7614 (tmm) cc_final: 0.7253 (tmm) REVERT: A 1051 TYR cc_start: 0.7964 (t80) cc_final: 0.6670 (t80) REVERT: A 1055 TYR cc_start: 0.7124 (m-10) cc_final: 0.6369 (m-80) REVERT: B 266 ILE cc_start: 0.6063 (OUTLIER) cc_final: 0.5536 (mm) REVERT: B 277 MET cc_start: 0.6280 (mmm) cc_final: 0.6000 (mtt) REVERT: B 352 TYR cc_start: 0.7645 (OUTLIER) cc_final: 0.7397 (m-10) REVERT: B 412 HIS cc_start: 0.3417 (OUTLIER) cc_final: 0.2067 (m-70) REVERT: B 418 MET cc_start: 0.8616 (tpt) cc_final: 0.8322 (tpt) REVERT: B 479 TYR cc_start: 0.5407 (OUTLIER) cc_final: 0.3799 (m-80) REVERT: B 665 MET cc_start: 0.7788 (mtm) cc_final: 0.7460 (mtm) REVERT: B 669 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8728 (mm) REVERT: B 788 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7698 (pp) REVERT: B 925 MET cc_start: 0.7684 (ppp) cc_final: 0.7463 (ppp) REVERT: B 1055 TYR cc_start: 0.7105 (m-10) cc_final: 0.6681 (m-80) REVERT: C 479 TYR cc_start: 0.5295 (OUTLIER) cc_final: 0.3822 (m-80) REVERT: C 642 MET cc_start: 0.8690 (tpp) cc_final: 0.8415 (tpp) REVERT: C 665 MET cc_start: 0.7744 (mtm) cc_final: 0.7418 (mtm) REVERT: C 669 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8731 (mm) REVERT: C 788 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7592 (pp) REVERT: C 1230 MET cc_start: 0.8545 (ttm) cc_final: 0.8283 (ttm) REVERT: D 479 TYR cc_start: 0.5132 (OUTLIER) cc_final: 0.3877 (m-80) REVERT: D 665 MET cc_start: 0.7847 (mtm) cc_final: 0.7540 (mtm) REVERT: D 669 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8730 (mm) REVERT: D 778 ILE cc_start: 0.9114 (pt) cc_final: 0.8899 (mt) REVERT: D 788 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7277 (pp) REVERT: D 1010 MET cc_start: 0.7634 (tmm) cc_final: 0.7177 (tmm) REVERT: D 1055 TYR cc_start: 0.7136 (m-80) cc_final: 0.6548 (m-80) REVERT: D 1150 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8291 (mp) outliers start: 148 outliers final: 98 residues processed: 473 average time/residue: 0.3814 time to fit residues: 301.7351 Evaluate side-chains 476 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 359 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1242 HIS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1178 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 895 VAL Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1009 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1115 ASN Chi-restraints excluded: chain C residue 1139 THR Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain C residue 1155 HIS Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 202 LYS Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1009 ASP Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1099 LEU Chi-restraints excluded: chain D residue 1150 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1242 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 252 optimal weight: 0.0870 chunk 182 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 290 optimal weight: 9.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32238 Z= 0.211 Angle : 0.574 12.231 43603 Z= 0.278 Chirality : 0.039 0.193 4897 Planarity : 0.004 0.056 5416 Dihedral : 7.061 65.444 4635 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.01 % Allowed : 16.63 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.14), residues: 3770 helix: 1.90 (0.11), residues: 2344 sheet: -0.40 (0.33), residues: 231 loop : -1.06 (0.18), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 763 HIS 0.003 0.001 HIS A 240 PHE 0.036 0.001 PHE A 913 TYR 0.015 0.001 TYR D 865 ARG 0.015 0.000 ARG D 985 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 364 time to evaluate : 3.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.7394 (OUTLIER) cc_final: 0.7153 (m-10) REVERT: A 479 TYR cc_start: 0.5500 (OUTLIER) cc_final: 0.4357 (m-80) REVERT: A 642 MET cc_start: 0.8697 (tpp) cc_final: 0.8463 (tpp) REVERT: A 665 MET cc_start: 0.7719 (mtm) cc_final: 0.7373 (mtm) REVERT: A 669 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8813 (mm) REVERT: A 788 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7254 (pp) REVERT: A 932 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8801 (mm) REVERT: A 948 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8763 (tp) REVERT: A 1010 MET cc_start: 0.7601 (tmm) cc_final: 0.7211 (tmm) REVERT: A 1051 TYR cc_start: 0.7921 (t80) cc_final: 0.6724 (t80) REVERT: A 1055 TYR cc_start: 0.7219 (m-10) cc_final: 0.6406 (m-10) REVERT: A 1138 MET cc_start: 0.8397 (mmt) cc_final: 0.8171 (mpp) REVERT: B 266 ILE cc_start: 0.6031 (OUTLIER) cc_final: 0.5504 (mm) REVERT: B 277 MET cc_start: 0.6226 (mmm) cc_final: 0.5991 (mtt) REVERT: B 412 HIS cc_start: 0.3555 (OUTLIER) cc_final: 0.2175 (m-70) REVERT: B 418 MET cc_start: 0.8613 (tpt) cc_final: 0.8299 (tpt) REVERT: B 479 TYR cc_start: 0.5347 (OUTLIER) cc_final: 0.3762 (m-80) REVERT: B 642 MET cc_start: 0.8662 (tpp) cc_final: 0.8427 (tpp) REVERT: B 665 MET cc_start: 0.7703 (mtm) cc_final: 0.7363 (mtm) REVERT: B 669 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8800 (mm) REVERT: B 788 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7794 (pp) REVERT: B 925 MET cc_start: 0.7714 (ppp) cc_final: 0.7435 (ppp) REVERT: B 1055 TYR cc_start: 0.7132 (m-10) cc_final: 0.6673 (m-10) REVERT: C 479 TYR cc_start: 0.5147 (OUTLIER) cc_final: 0.3755 (m-80) REVERT: C 665 MET cc_start: 0.7653 (mtm) cc_final: 0.7334 (mtm) REVERT: C 669 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8800 (mm) REVERT: C 788 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7567 (pp) REVERT: D 479 TYR cc_start: 0.5072 (OUTLIER) cc_final: 0.3882 (m-80) REVERT: D 642 MET cc_start: 0.8648 (tpp) cc_final: 0.8398 (tpp) REVERT: D 665 MET cc_start: 0.7759 (mtm) cc_final: 0.7455 (mtm) REVERT: D 669 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8790 (mm) REVERT: D 778 ILE cc_start: 0.9100 (pt) cc_final: 0.8894 (mt) REVERT: D 788 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7251 (pp) REVERT: D 1010 MET cc_start: 0.7636 (tmm) cc_final: 0.7170 (tmm) REVERT: D 1150 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8285 (mp) outliers start: 136 outliers final: 98 residues processed: 468 average time/residue: 0.3734 time to fit residues: 294.7445 Evaluate side-chains 475 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 359 time to evaluate : 3.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1022 MET Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain A residue 1178 ASP Chi-restraints excluded: chain A residue 1242 HIS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 646 VAL Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1021 LEU Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1178 ASP Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 633 HIS Chi-restraints excluded: chain C residue 646 VAL Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1009 ASP Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain C residue 1155 HIS Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 216 THR Chi-restraints excluded: chain D residue 242 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 794 ASN Chi-restraints excluded: chain D residue 895 VAL Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1009 ASP Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1021 LEU Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1150 LEU Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1155 HIS Chi-restraints excluded: chain D residue 1242 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 2.9990 chunk 354 optimal weight: 0.6980 chunk 323 optimal weight: 2.9990 chunk 344 optimal weight: 2.9990 chunk 207 optimal weight: 0.0000 chunk 150 optimal weight: 0.9980 chunk 270 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 311 optimal weight: 0.0770 chunk 326 optimal weight: 0.7980 chunk 343 optimal weight: 0.8980 overall best weight: 0.4942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1116 ASN B1115 ASN C 482 GLN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 32238 Z= 0.145 Angle : 0.565 14.899 43603 Z= 0.269 Chirality : 0.037 0.204 4897 Planarity : 0.004 0.055 5416 Dihedral : 6.800 59.707 4635 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.39 % Allowed : 17.22 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.14), residues: 3770 helix: 2.07 (0.11), residues: 2340 sheet: -0.34 (0.34), residues: 231 loop : -1.02 (0.18), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C1052 HIS 0.006 0.001 HIS D1155 PHE 0.034 0.001 PHE A 913 TYR 0.010 0.001 TYR B 380 ARG 0.014 0.000 ARG D 985 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 377 time to evaluate : 3.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.7290 (OUTLIER) cc_final: 0.7027 (m-10) REVERT: A 479 TYR cc_start: 0.5398 (OUTLIER) cc_final: 0.4273 (m-80) REVERT: A 568 MET cc_start: 0.8948 (mmm) cc_final: 0.8722 (mmm) REVERT: A 665 MET cc_start: 0.7805 (mtm) cc_final: 0.7470 (mtm) REVERT: A 669 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8798 (mm) REVERT: A 788 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7236 (pp) REVERT: A 932 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8730 (mm) REVERT: A 1010 MET cc_start: 0.7552 (tmm) cc_final: 0.7131 (tmm) REVERT: A 1051 TYR cc_start: 0.7916 (t80) cc_final: 0.6899 (t80) REVERT: A 1055 TYR cc_start: 0.7228 (m-10) cc_final: 0.6437 (m-10) REVERT: A 1138 MET cc_start: 0.8360 (mmt) cc_final: 0.8101 (mpp) REVERT: B 154 LYS cc_start: 0.8485 (mmtt) cc_final: 0.8190 (mmtm) REVERT: B 266 ILE cc_start: 0.5920 (OUTLIER) cc_final: 0.5417 (mm) REVERT: B 352 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7287 (m-10) REVERT: B 412 HIS cc_start: 0.3423 (OUTLIER) cc_final: 0.2043 (m-70) REVERT: B 479 TYR cc_start: 0.4891 (OUTLIER) cc_final: 0.3239 (m-80) REVERT: B 568 MET cc_start: 0.8956 (mmm) cc_final: 0.8733 (mmm) REVERT: B 665 MET cc_start: 0.7808 (mtm) cc_final: 0.7477 (mtm) REVERT: B 669 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8774 (mm) REVERT: B 788 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7765 (pp) REVERT: B 925 MET cc_start: 0.7598 (ppp) cc_final: 0.7288 (ppp) REVERT: B 1055 TYR cc_start: 0.7089 (m-10) cc_final: 0.6751 (m-10) REVERT: C 420 CYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7834 (t) REVERT: C 479 TYR cc_start: 0.5292 (OUTLIER) cc_final: 0.3912 (m-80) REVERT: C 568 MET cc_start: 0.9031 (mmm) cc_final: 0.8801 (mmm) REVERT: C 665 MET cc_start: 0.7780 (mtm) cc_final: 0.7442 (mtm) REVERT: C 669 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8784 (mm) REVERT: C 788 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7534 (pp) REVERT: D 154 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8340 (mmtm) REVERT: D 479 TYR cc_start: 0.5413 (OUTLIER) cc_final: 0.4018 (m-80) REVERT: D 568 MET cc_start: 0.8937 (mmm) cc_final: 0.8699 (mmm) REVERT: D 665 MET cc_start: 0.7795 (mtm) cc_final: 0.7469 (mtm) REVERT: D 669 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8780 (mm) REVERT: D 778 ILE cc_start: 0.9155 (pt) cc_final: 0.8926 (mt) REVERT: D 788 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7228 (pp) REVERT: D 1010 MET cc_start: 0.7599 (tmm) cc_final: 0.7158 (tmm) outliers start: 115 outliers final: 71 residues processed: 464 average time/residue: 0.3778 time to fit residues: 293.3347 Evaluate side-chains 453 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 364 time to evaluate : 3.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 794 ASN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1242 HIS Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1095 MET Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 794 ASN Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1009 ASP Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1099 LEU Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain C residue 1186 THR Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1155 HIS Chi-restraints excluded: chain D residue 1242 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.5980 chunk 364 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 253 optimal weight: 0.0980 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 2.9990 chunk 304 optimal weight: 7.9990 chunk 31 optimal weight: 0.1980 chunk 235 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1115 ASN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 ASN ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32238 Z= 0.172 Angle : 0.589 13.966 43603 Z= 0.277 Chirality : 0.038 0.185 4897 Planarity : 0.004 0.055 5416 Dihedral : 6.652 59.866 4633 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.89 % Allowed : 17.63 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.14), residues: 3770 helix: 2.09 (0.11), residues: 2339 sheet: -0.24 (0.33), residues: 228 loop : -0.99 (0.18), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 763 HIS 0.008 0.001 HIS C 240 PHE 0.033 0.001 PHE A 913 TYR 0.017 0.001 TYR C 865 ARG 0.013 0.000 ARG D 985 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7540 Ramachandran restraints generated. 3770 Oldfield, 0 Emsley, 3770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 370 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.7014 (m-10) REVERT: A 479 TYR cc_start: 0.5404 (OUTLIER) cc_final: 0.4296 (m-80) REVERT: A 665 MET cc_start: 0.7688 (mtm) cc_final: 0.7356 (mtm) REVERT: A 669 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8827 (mm) REVERT: A 788 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7240 (pp) REVERT: A 932 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8692 (mm) REVERT: A 1010 MET cc_start: 0.7579 (tmm) cc_final: 0.7226 (tmm) REVERT: A 1051 TYR cc_start: 0.8014 (t80) cc_final: 0.6988 (t80) REVERT: A 1055 TYR cc_start: 0.7253 (m-10) cc_final: 0.6402 (m-10) REVERT: A 1138 MET cc_start: 0.8351 (mmt) cc_final: 0.8100 (mpp) REVERT: B 154 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8296 (mmmt) REVERT: B 266 ILE cc_start: 0.5931 (OUTLIER) cc_final: 0.5432 (mm) REVERT: B 352 TYR cc_start: 0.7588 (OUTLIER) cc_final: 0.7307 (m-10) REVERT: B 412 HIS cc_start: 0.3505 (OUTLIER) cc_final: 0.2112 (m-70) REVERT: B 479 TYR cc_start: 0.4899 (OUTLIER) cc_final: 0.3259 (m-80) REVERT: B 665 MET cc_start: 0.7667 (mtm) cc_final: 0.7331 (mtm) REVERT: B 669 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8799 (mm) REVERT: B 788 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7784 (pp) REVERT: B 925 MET cc_start: 0.7594 (ppp) cc_final: 0.7321 (ppp) REVERT: B 1055 TYR cc_start: 0.7086 (m-10) cc_final: 0.6704 (m-10) REVERT: C 420 CYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7847 (t) REVERT: C 479 TYR cc_start: 0.5305 (OUTLIER) cc_final: 0.3913 (m-80) REVERT: C 665 MET cc_start: 0.7644 (mtm) cc_final: 0.7317 (mtm) REVERT: C 669 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8798 (mm) REVERT: C 788 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7551 (pp) REVERT: D 479 TYR cc_start: 0.5424 (OUTLIER) cc_final: 0.4045 (m-80) REVERT: D 665 MET cc_start: 0.7665 (mtm) cc_final: 0.7332 (mtm) REVERT: D 669 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8797 (mm) REVERT: D 778 ILE cc_start: 0.9170 (pt) cc_final: 0.8958 (mt) REVERT: D 788 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7247 (pp) REVERT: D 924 LEU cc_start: 0.8661 (pp) cc_final: 0.8391 (mt) REVERT: D 1010 MET cc_start: 0.7626 (tmm) cc_final: 0.7170 (tmm) REVERT: D 1055 TYR cc_start: 0.7065 (m-80) cc_final: 0.6532 (m-80) outliers start: 98 outliers final: 75 residues processed: 448 average time/residue: 0.3984 time to fit residues: 297.6778 Evaluate side-chains 458 residues out of total 3391 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 365 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 205 PHE Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 352 TYR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 470 ASP Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 690 ASP Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1100 LEU Chi-restraints excluded: chain A residue 1150 LEU Chi-restraints excluded: chain A residue 1151 ILE Chi-restraints excluded: chain A residue 1155 HIS Chi-restraints excluded: chain A residue 1186 THR Chi-restraints excluded: chain A residue 1242 HIS Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 205 PHE Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 240 HIS Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 352 TYR Chi-restraints excluded: chain B residue 373 ILE Chi-restraints excluded: chain B residue 412 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain B residue 479 TYR Chi-restraints excluded: chain B residue 502 ASP Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain B residue 736 THR Chi-restraints excluded: chain B residue 775 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 794 ASN Chi-restraints excluded: chain B residue 983 TYR Chi-restraints excluded: chain B residue 996 LEU Chi-restraints excluded: chain B residue 1012 TYR Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1058 VAL Chi-restraints excluded: chain B residue 1115 ASN Chi-restraints excluded: chain B residue 1150 LEU Chi-restraints excluded: chain B residue 1151 ILE Chi-restraints excluded: chain B residue 1242 HIS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 376 PHE Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 420 CYS Chi-restraints excluded: chain C residue 440 ILE Chi-restraints excluded: chain C residue 470 ASP Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 775 LEU Chi-restraints excluded: chain C residue 788 LEU Chi-restraints excluded: chain C residue 983 TYR Chi-restraints excluded: chain C residue 1009 ASP Chi-restraints excluded: chain C residue 1014 VAL Chi-restraints excluded: chain C residue 1151 ILE Chi-restraints excluded: chain C residue 1186 THR Chi-restraints excluded: chain C residue 1242 HIS Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 376 PHE Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 470 ASP Chi-restraints excluded: chain D residue 479 TYR Chi-restraints excluded: chain D residue 502 ASP Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 983 TYR Chi-restraints excluded: chain D residue 1012 TYR Chi-restraints excluded: chain D residue 1014 VAL Chi-restraints excluded: chain D residue 1022 MET Chi-restraints excluded: chain D residue 1091 VAL Chi-restraints excluded: chain D residue 1115 ASN Chi-restraints excluded: chain D residue 1151 ILE Chi-restraints excluded: chain D residue 1155 HIS Chi-restraints excluded: chain D residue 1242 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 5.9990 chunk 324 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 280 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 313 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 ASN B1115 ASN ** C1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1062 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1115 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.108718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.088567 restraints weight = 71041.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.090744 restraints weight = 45356.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.092248 restraints weight = 33940.423| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32238 Z= 0.170 Angle : 0.582 14.003 43603 Z= 0.275 Chirality : 0.038 0.189 4897 Planarity : 0.004 0.055 5416 Dihedral : 6.513 58.981 4627 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.98 % Allowed : 17.93 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.54 (0.14), residues: 3770 helix: 2.12 (0.11), residues: 2338 sheet: -0.24 (0.33), residues: 228 loop : -0.97 (0.18), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 763 HIS 0.007 0.001 HIS C 240 PHE 0.032 0.001 PHE A 913 TYR 0.011 0.001 TYR A 983 ARG 0.013 0.000 ARG D 985 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6309.72 seconds wall clock time: 116 minutes 14.94 seconds (6974.94 seconds total)