Starting phenix.real_space_refine on Fri Apr 12 21:09:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p40_13190/04_2024/7p40_13190_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p40_13190/04_2024/7p40_13190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p40_13190/04_2024/7p40_13190.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p40_13190/04_2024/7p40_13190.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p40_13190/04_2024/7p40_13190_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p40_13190/04_2024/7p40_13190_neut.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 16881 2.51 5 N 4527 2.21 5 O 4926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26466 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 29, 'ASP:plan': 25, 'PHE:plan': 8, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 437 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "C" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 932 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "D" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "E" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 29, 'ASP:plan': 25, 'PHE:plan': 8, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 437 Chain: "F" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 932 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "G" Number of atoms: 7064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7064 Classifications: {'peptide': 998} Incomplete info: {'truncation_to_alanine': 244} Link IDs: {'PTRANS': 53, 'TRANS': 944} Chain breaks: 7 Unresolved non-hydrogen bonds: 747 Unresolved non-hydrogen angles: 959 Unresolved non-hydrogen dihedrals: 582 Unresolved non-hydrogen chiralities: 75 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 29, 'ASP:plan': 25, 'PHE:plan': 8, 'GLU:plan': 17, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 437 Chain: "H" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} Chain: "I" Number of atoms: 932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 932 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Time building chain proxies: 13.87, per 1000 atoms: 0.52 Number of scatterers: 26466 At special positions: 0 Unit cell: (134.48, 132.84, 227.96, 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 132 16.00 O 4926 8.00 N 4527 7.00 C 16881 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 100B" distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.04 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS F 97 " - pdb=" SG CYS F 100B" distance=2.03 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.04 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.03 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.03 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 97 " - pdb=" SG CYS I 100B" distance=2.03 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: 9.82 Conformation dependent library (CDL) restraints added in 5.3 seconds 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6840 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 51 sheets defined 21.3% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.918A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.530A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.500A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.655A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 3.624A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.134A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 29 through 31 No H-bonds generated for 'chain 'B' and resid 29 through 31' Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 364 through 371 removed outlier: 3.918A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 390 Processing helix chain 'E' and resid 406 through 410 Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 616 through 620 removed outlier: 3.531A pdb=" N VAL E 620 " --> pdb=" O CYS E 617 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 754 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 758 through 783 removed outlier: 3.500A pdb=" N ASP E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 825 Processing helix chain 'E' and resid 866 through 885 Processing helix chain 'E' and resid 897 through 909 removed outlier: 3.655A pdb=" N ILE E 909 " --> pdb=" O ARG E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 919 Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 945 through 967 removed outlier: 3.626A pdb=" N SER E 967 " --> pdb=" O VAL E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 984 Processing helix chain 'E' and resid 985 through 1033 removed outlier: 4.135A pdb=" N VAL E 991 " --> pdb=" O PRO E 987 " (cutoff:3.500A) Processing helix chain 'E' and resid 1140 through 1145 Processing helix chain 'G' and resid 294 through 304 Processing helix chain 'G' and resid 338 through 343 Processing helix chain 'G' and resid 364 through 371 removed outlier: 3.919A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 390 Processing helix chain 'G' and resid 406 through 410 Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'G' and resid 616 through 620 removed outlier: 3.529A pdb=" N VAL G 620 " --> pdb=" O CYS G 617 " (cutoff:3.500A) Processing helix chain 'G' and resid 737 through 743 Processing helix chain 'G' and resid 746 through 754 Processing helix chain 'G' and resid 755 through 757 No H-bonds generated for 'chain 'G' and resid 755 through 757' Processing helix chain 'G' and resid 758 through 783 removed outlier: 3.501A pdb=" N ASP G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 825 Processing helix chain 'G' and resid 866 through 885 Processing helix chain 'G' and resid 897 through 909 removed outlier: 3.657A pdb=" N ILE G 909 " --> pdb=" O ARG G 905 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 919 Processing helix chain 'G' and resid 919 through 941 Processing helix chain 'G' and resid 945 through 967 removed outlier: 3.625A pdb=" N SER G 967 " --> pdb=" O VAL G 963 " (cutoff:3.500A) Processing helix chain 'G' and resid 976 through 984 Processing helix chain 'G' and resid 985 through 1033 removed outlier: 4.134A pdb=" N VAL G 991 " --> pdb=" O PRO G 987 " (cutoff:3.500A) Processing helix chain 'G' and resid 1140 through 1145 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.259A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.368A pdb=" N PHE A 43 " --> pdb=" O ARG G 567 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP G 574 " --> pdb=" O ILE G 587 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLU G 324 " --> pdb=" O ASN G 540 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASN G 542 " --> pdb=" O GLU G 324 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE G 326 " --> pdb=" O ASN G 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.736A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.787A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 3.525A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.805A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.211A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.223A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.223A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.438A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AB7, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.821A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AB9, first strand: chain 'C' and resid 9 through 12 removed outlier: 3.864A pdb=" N GLY C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.822A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 28 through 30 removed outlier: 8.259A pdb=" N ASN E 61 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR E 269 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N SER E 205 " --> pdb=" O PRO E 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 48 through 55 removed outlier: 7.736A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 84 through 85 removed outlier: 5.788A pdb=" N ARG E 102 " --> pdb=" O ASN E 121 " (cutoff:3.500A) removed outlier: 11.297A pdb=" N VAL E 126 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLU E 169 " --> pdb=" O VAL E 126 " (cutoff:3.500A) removed outlier: 11.488A pdb=" N ILE E 128 " --> pdb=" O THR E 167 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR E 167 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL E 130 " --> pdb=" O ASN E 165 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASN E 165 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLU E 132 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA E 163 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN E 134 " --> pdb=" O SER E 161 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N VAL E 159 " --> pdb=" O CYS E 136 " (cutoff:3.500A) removed outlier: 11.423A pdb=" N ASP E 138 " --> pdb=" O PHE E 157 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N PHE E 157 " --> pdb=" O ASP E 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 311 through 319 removed outlier: 3.525A pdb=" N THR E 599 " --> pdb=" O GLY E 311 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 324 through 328 removed outlier: 6.805A pdb=" N GLU E 324 " --> pdb=" O ASN E 540 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N ASN E 542 " --> pdb=" O GLU E 324 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE E 326 " --> pdb=" O ASN E 542 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.210A pdb=" N ALA E 672 " --> pdb=" O PRO E 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.223A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY E1059 " --> pdb=" O SER E1055 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N SER E1055 " --> pdb=" O GLY E1059 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL E1061 " --> pdb=" O PRO E1053 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU E1063 " --> pdb=" O SER E1051 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER E1051 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL E1065 " --> pdb=" O LEU E1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 711 through 728 removed outlier: 6.223A pdb=" N GLN E1071 " --> pdb=" O THR E 716 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE E 718 " --> pdb=" O PRO E1069 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE E 720 " --> pdb=" O TYR E1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR E1067 " --> pdb=" O ILE E 720 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL E 722 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL E1065 " --> pdb=" O VAL E 722 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR E 724 " --> pdb=" O LEU E1063 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU E1063 " --> pdb=" O THR E 724 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE E 726 " --> pdb=" O VAL E1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL E1061 " --> pdb=" O ILE E 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY E1059 " --> pdb=" O PRO E 728 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 733 through 736 removed outlier: 4.503A pdb=" N LYS E 733 " --> pdb=" O LEU E 861 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 1120 through 1125 removed outlier: 4.439A pdb=" N ALA E1087 " --> pdb=" O SER E1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 3 through 5 Processing sheet with id=AD8, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.865A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 28 through 30 removed outlier: 8.259A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N SER G 205 " --> pdb=" O PRO G 225 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 48 through 55 removed outlier: 7.735A pdb=" N THR G 274 " --> pdb=" O ASP G 290 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP G 290 " --> pdb=" O THR G 274 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU G 276 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA G 288 " --> pdb=" O LEU G 276 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS G 278 " --> pdb=" O THR G 286 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 84 through 85 removed outlier: 5.788A pdb=" N ARG G 102 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N VAL G 126 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 9.884A pdb=" N GLU G 169 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 11.490A pdb=" N ILE G 128 " --> pdb=" O THR G 167 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR G 167 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL G 130 " --> pdb=" O ASN G 165 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASN G 165 " --> pdb=" O VAL G 130 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLU G 132 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA G 163 " --> pdb=" O GLU G 132 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN G 134 " --> pdb=" O SER G 161 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL G 159 " --> pdb=" O CYS G 136 " (cutoff:3.500A) removed outlier: 11.424A pdb=" N ASP G 138 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 10.217A pdb=" N PHE G 157 " --> pdb=" O ASP G 138 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 311 through 319 removed outlier: 3.525A pdb=" N THR G 599 " --> pdb=" O GLY G 311 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL G 595 " --> pdb=" O THR G 315 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN G 317 " --> pdb=" O GLY G 593 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLY G 593 " --> pdb=" O ASN G 317 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLY G 594 " --> pdb=" O GLN G 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 354 through 358 Processing sheet with id=AE5, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'G' and resid 654 through 655 removed outlier: 6.210A pdb=" N ALA G 672 " --> pdb=" O PRO G 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 711 through 728 removed outlier: 6.223A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY G1059 " --> pdb=" O SER G1055 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N SER G1055 " --> pdb=" O GLY G1059 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL G1061 " --> pdb=" O PRO G1053 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU G1063 " --> pdb=" O SER G1051 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N SER G1051 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL G1065 " --> pdb=" O LEU G1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 711 through 728 removed outlier: 6.223A pdb=" N GLN G1071 " --> pdb=" O THR G 716 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N PHE G 718 " --> pdb=" O PRO G1069 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE G 720 " --> pdb=" O TYR G1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR G1067 " --> pdb=" O ILE G 720 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL G 722 " --> pdb=" O VAL G1065 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL G1065 " --> pdb=" O VAL G 722 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR G 724 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LEU G1063 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE G 726 " --> pdb=" O VAL G1061 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL G1061 " --> pdb=" O ILE G 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLY G1059 " --> pdb=" O PRO G 728 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 733 through 736 removed outlier: 4.504A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 1120 through 1125 removed outlier: 4.439A pdb=" N ALA G1087 " --> pdb=" O SER G1123 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AF4, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.821A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 3 through 5 Processing sheet with id=AF6, first strand: chain 'I' and resid 9 through 12 removed outlier: 3.865A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) 1201 hydrogen bonds defined for protein. 3252 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: 14.21 Time building geometry restraints manager: 10.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8681 1.34 - 1.46: 5046 1.46 - 1.58: 13162 1.58 - 1.70: 0 1.70 - 1.81: 168 Bond restraints: 27057 Sorted by residual: bond pdb=" N SER B 94 " pdb=" CA SER B 94 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.04e-02 9.25e+03 9.73e+00 bond pdb=" N SER D 94 " pdb=" CA SER D 94 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.04e-02 9.25e+03 8.28e+00 bond pdb=" N SER H 94 " pdb=" CA SER H 94 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.04e-02 9.25e+03 8.24e+00 bond pdb=" N SER D 93 " pdb=" CA SER D 93 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.29e-02 6.01e+03 7.73e+00 bond pdb=" N TRP B 96 " pdb=" CA TRP B 96 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.21e-02 6.83e+03 7.43e+00 ... (remaining 27052 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.38: 845 106.38 - 113.39: 14396 113.39 - 120.40: 9619 120.40 - 127.40: 11861 127.40 - 134.41: 260 Bond angle restraints: 36981 Sorted by residual: angle pdb=" N GLN B 90 " pdb=" CA GLN B 90 " pdb=" C GLN B 90 " ideal model delta sigma weight residual 109.40 103.77 5.63 1.63e+00 3.76e-01 1.19e+01 angle pdb=" N GLN I 105 " pdb=" CA GLN I 105 " pdb=" C GLN I 105 " ideal model delta sigma weight residual 114.56 110.18 4.38 1.27e+00 6.20e-01 1.19e+01 angle pdb=" N GLN F 105 " pdb=" CA GLN F 105 " pdb=" C GLN F 105 " ideal model delta sigma weight residual 114.56 110.21 4.35 1.27e+00 6.20e-01 1.17e+01 angle pdb=" N GLN D 90 " pdb=" CA GLN D 90 " pdb=" C GLN D 90 " ideal model delta sigma weight residual 109.40 103.84 5.56 1.63e+00 3.76e-01 1.16e+01 angle pdb=" N GLN C 105 " pdb=" CA GLN C 105 " pdb=" C GLN C 105 " ideal model delta sigma weight residual 114.56 110.25 4.31 1.27e+00 6.20e-01 1.15e+01 ... (remaining 36976 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 15039 17.28 - 34.56: 735 34.56 - 51.84: 157 51.84 - 69.12: 47 69.12 - 86.40: 24 Dihedral angle restraints: 16002 sinusoidal: 5367 harmonic: 10635 Sorted by residual: dihedral pdb=" CB CYS E 538 " pdb=" SG CYS E 538 " pdb=" SG CYS E 590 " pdb=" CB CYS E 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.46 66.46 1 1.00e+01 1.00e-02 5.77e+01 dihedral pdb=" CB CYS G 538 " pdb=" SG CYS G 538 " pdb=" SG CYS G 590 " pdb=" CB CYS G 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.41 66.41 1 1.00e+01 1.00e-02 5.76e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.40 66.40 1 1.00e+01 1.00e-02 5.76e+01 ... (remaining 15999 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3353 0.050 - 0.101: 717 0.101 - 0.151: 199 0.151 - 0.202: 1 0.202 - 0.252: 5 Chirality restraints: 4275 Sorted by residual: chirality pdb=" CB ILE G 101 " pdb=" CA ILE G 101 " pdb=" CG1 ILE G 101 " pdb=" CG2 ILE G 101 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE A 101 " pdb=" CA ILE A 101 " pdb=" CG1 ILE A 101 " pdb=" CG2 ILE A 101 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE E 101 " pdb=" CA ILE E 101 " pdb=" CG1 ILE E 101 " pdb=" CG2 ILE E 101 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 4272 not shown) Planarity restraints: 4848 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY D 92 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.57e+00 pdb=" C GLY D 92 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY D 92 " 0.018 2.00e-02 2.50e+03 pdb=" N SER D 93 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 92 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C GLY B 92 " -0.045 2.00e-02 2.50e+03 pdb=" O GLY B 92 " 0.017 2.00e-02 2.50e+03 pdb=" N SER B 93 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER H 7 " -0.041 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO H 8 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO H 8 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO H 8 " -0.034 5.00e-02 4.00e+02 ... (remaining 4845 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3326 2.76 - 3.29: 24629 3.29 - 3.83: 42834 3.83 - 4.36: 47435 4.36 - 4.90: 85811 Nonbonded interactions: 204035 Sorted by model distance: nonbonded pdb=" O GLN E 804 " pdb=" OG SER E 816 " model vdw 2.221 2.440 nonbonded pdb=" O GLN A 804 " pdb=" OG SER A 816 " model vdw 2.222 2.440 nonbonded pdb=" O GLN G 804 " pdb=" OG SER G 816 " model vdw 2.223 2.440 nonbonded pdb=" O GLU G1092 " pdb=" NH1 ARG G1107 " model vdw 2.284 2.520 nonbonded pdb=" O GLU A1092 " pdb=" NH1 ARG A1107 " model vdw 2.284 2.520 ... (remaining 204030 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' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } 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: 1.230 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: 7.300 Check model and map are aligned: 0.430 Set scattering table: 0.300 Process input model: 74.820 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.190 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 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 : 0.003 0.036 27057 Z= 0.171 Angle : 0.534 6.847 36981 Z= 0.291 Chirality : 0.045 0.252 4275 Planarity : 0.004 0.061 4848 Dihedral : 11.695 86.401 9018 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.39 % Favored : 96.58 % Rotamer: Outliers : 0.24 % Allowed : 0.16 % Favored : 99.59 % 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: 0.85 (0.14), residues: 3627 helix: 2.58 (0.20), residues: 690 sheet: 0.84 (0.17), residues: 912 loop : -0.26 (0.14), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 103 HIS 0.002 0.001 HIS G1064 PHE 0.013 0.001 PHE E 906 TYR 0.016 0.001 TYR H 36 ARG 0.002 0.000 ARG F 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 397 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 LEU cc_start: 0.8217 (mt) cc_final: 0.8015 (mp) REVERT: A 577 ARG cc_start: 0.7144 (ttm-80) cc_final: 0.6794 (ttm-80) REVERT: A 699 LEU cc_start: 0.8585 (mt) cc_final: 0.8378 (mt) REVERT: C 73 MET cc_start: 0.0367 (mmm) cc_final: -0.2182 (ttm) REVERT: E 423 TYR cc_start: 0.5579 (t80) cc_final: 0.5302 (t80) REVERT: E 741 TYR cc_start: 0.8913 (t80) cc_final: 0.8509 (t80) REVERT: E 902 MET cc_start: 0.7256 (tpp) cc_final: 0.6908 (mmm) REVERT: F 59 TYR cc_start: 0.3733 (m-80) cc_final: 0.3357 (m-80) REVERT: F 80 MET cc_start: 0.2189 (ppp) cc_final: 0.0033 (tmm) REVERT: G 274 THR cc_start: 0.8512 (m) cc_final: 0.8283 (p) REVERT: G 731 MET cc_start: 0.7374 (ptm) cc_final: 0.7112 (ptm) REVERT: G 742 ILE cc_start: 0.8933 (mt) cc_final: 0.8587 (mt) REVERT: G 1047 TYR cc_start: 0.8242 (m-80) cc_final: 0.7902 (m-10) outliers start: 6 outliers final: 0 residues processed: 403 average time/residue: 0.3527 time to fit residues: 230.6069 Evaluate side-chains 225 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 0.9990 chunk 275 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 284 optimal weight: 20.0000 chunk 110 optimal weight: 3.9990 chunk 173 optimal weight: 30.0000 chunk 211 optimal weight: 2.9990 chunk 329 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 755 GLN E 218 GLN E 321 GLN E 901 GLN ** F 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 HIS G1010 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 27057 Z= 0.298 Angle : 0.583 9.175 36981 Z= 0.303 Chirality : 0.046 0.194 4275 Planarity : 0.005 0.047 4848 Dihedral : 3.853 17.246 3900 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.01 % Allowed : 8.55 % Favored : 90.44 % 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: 0.74 (0.14), residues: 3627 helix: 2.23 (0.20), residues: 681 sheet: 1.03 (0.17), residues: 867 loop : -0.32 (0.14), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 47 HIS 0.009 0.001 HIS G1064 PHE 0.029 0.002 PHE E 392 TYR 0.025 0.002 TYR C 79 ARG 0.005 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 232 time to evaluate : 3.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7940 (tp) cc_final: 0.7730 (tp) REVERT: A 275 PHE cc_start: 0.7689 (m-80) cc_final: 0.7207 (m-10) REVERT: A 577 ARG cc_start: 0.7313 (ttm-80) cc_final: 0.7029 (ttm-80) REVERT: A 699 LEU cc_start: 0.8652 (mt) cc_final: 0.8308 (mt) REVERT: A 900 MET cc_start: 0.6975 (mtm) cc_final: 0.6449 (mtm) REVERT: C 2 MET cc_start: 0.4728 (mmt) cc_final: 0.3781 (mmt) REVERT: C 73 MET cc_start: 0.0982 (mmm) cc_final: -0.2117 (ttm) REVERT: C 77 THR cc_start: 0.2437 (OUTLIER) cc_final: 0.1994 (m) REVERT: E 223 LEU cc_start: 0.6467 (mp) cc_final: 0.6243 (mt) REVERT: E 423 TYR cc_start: 0.5689 (t80) cc_final: 0.5423 (t80) REVERT: E 873 TYR cc_start: 0.7787 (m-80) cc_final: 0.7418 (m-80) REVERT: E 902 MET cc_start: 0.7773 (tpp) cc_final: 0.7496 (mmm) REVERT: F 59 TYR cc_start: 0.3232 (m-80) cc_final: 0.2815 (m-80) REVERT: F 80 MET cc_start: 0.2633 (ppp) cc_final: 0.0364 (tmm) REVERT: G 421 TYR cc_start: 0.6596 (m-80) cc_final: 0.6319 (m-10) REVERT: G 571 ASP cc_start: 0.6975 (t0) cc_final: 0.6748 (t0) REVERT: G 902 MET cc_start: 0.7953 (mmm) cc_final: 0.7663 (mmm) REVERT: G 1047 TYR cc_start: 0.8198 (m-80) cc_final: 0.7928 (m-10) REVERT: I 2 MET cc_start: 0.2559 (ptt) cc_final: 0.2215 (pmm) outliers start: 25 outliers final: 17 residues processed: 252 average time/residue: 0.3529 time to fit residues: 149.5148 Evaluate side-chains 210 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 1001 LEU Chi-restraints excluded: chain G residue 207 HIS Chi-restraints excluded: chain G residue 533 LEU Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 1116 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 183 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 274 optimal weight: 40.0000 chunk 224 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 330 optimal weight: 0.5980 chunk 356 optimal weight: 6.9990 chunk 294 optimal weight: 0.6980 chunk 327 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 264 optimal weight: 3.9990 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 762 GLN A 901 GLN E 901 GLN G 207 HIS ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27057 Z= 0.171 Angle : 0.512 10.121 36981 Z= 0.262 Chirality : 0.045 0.196 4275 Planarity : 0.004 0.060 4848 Dihedral : 3.657 19.192 3900 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.34 % Allowed : 10.17 % Favored : 88.50 % 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: 0.76 (0.14), residues: 3627 helix: 2.36 (0.20), residues: 681 sheet: 0.91 (0.17), residues: 903 loop : -0.31 (0.14), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 50 HIS 0.008 0.001 HIS G 207 PHE 0.022 0.001 PHE E 92 TYR 0.019 0.001 TYR C 79 ARG 0.002 0.000 ARG E 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 214 time to evaluate : 3.074 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.7889 (tp) cc_final: 0.7685 (tp) REVERT: A 577 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.7332 (ttm-80) REVERT: A 699 LEU cc_start: 0.8694 (mt) cc_final: 0.8407 (mt) REVERT: A 906 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.6627 (m-10) REVERT: A 970 PHE cc_start: 0.8587 (m-80) cc_final: 0.8178 (m-10) REVERT: C 73 MET cc_start: 0.1419 (mmm) cc_final: -0.1646 (ttp) REVERT: C 77 THR cc_start: 0.1238 (OUTLIER) cc_final: 0.0558 (m) REVERT: C 108 MET cc_start: 0.2688 (mpp) cc_final: -0.0439 (mmt) REVERT: E 400 PHE cc_start: 0.6282 (p90) cc_final: 0.5887 (p90) REVERT: E 423 TYR cc_start: 0.5311 (t80) cc_final: 0.5066 (t80) REVERT: E 873 TYR cc_start: 0.7811 (m-80) cc_final: 0.7449 (m-80) REVERT: F 59 TYR cc_start: 0.3711 (m-80) cc_final: 0.2895 (m-80) REVERT: F 80 MET cc_start: 0.2482 (ppp) cc_final: 0.0319 (tmm) REVERT: G 421 TYR cc_start: 0.6208 (m-80) cc_final: 0.5987 (m-10) REVERT: G 742 ILE cc_start: 0.8991 (mt) cc_final: 0.8766 (mt) REVERT: G 902 MET cc_start: 0.7777 (mmm) cc_final: 0.7428 (mmm) REVERT: G 1047 TYR cc_start: 0.8166 (m-80) cc_final: 0.7912 (m-10) outliers start: 33 outliers final: 21 residues processed: 239 average time/residue: 0.3476 time to fit residues: 138.7535 Evaluate side-chains 212 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 189 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 533 LEU Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain G residue 207 HIS Chi-restraints excluded: chain G residue 317 ASN Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 961 THR Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 171 optimal weight: 0.4980 chunk 36 optimal weight: 50.0000 chunk 157 optimal weight: 20.0000 chunk 221 optimal weight: 0.7980 chunk 331 optimal weight: 0.7980 chunk 350 optimal weight: 4.9990 chunk 173 optimal weight: 30.0000 chunk 314 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27057 Z= 0.163 Angle : 0.508 10.432 36981 Z= 0.258 Chirality : 0.044 0.181 4275 Planarity : 0.004 0.046 4848 Dihedral : 3.558 18.382 3900 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.86 % Allowed : 11.18 % Favored : 86.96 % 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: 0.77 (0.14), residues: 3627 helix: 2.39 (0.20), residues: 681 sheet: 0.98 (0.17), residues: 873 loop : -0.33 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 50 HIS 0.011 0.001 HIS G 207 PHE 0.030 0.001 PHE A 392 TYR 0.016 0.001 TYR C 79 ARG 0.003 0.000 ARG G 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 208 time to evaluate : 2.872 Fit side-chains revert: symmetry clash REVERT: A 577 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.7182 (ttm-80) REVERT: A 699 LEU cc_start: 0.8701 (mt) cc_final: 0.8357 (mt) REVERT: A 906 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.6837 (m-10) REVERT: A 970 PHE cc_start: 0.8568 (m-80) cc_final: 0.8214 (m-10) REVERT: C 2 MET cc_start: 0.4654 (mmt) cc_final: 0.3994 (mmt) REVERT: C 73 MET cc_start: 0.0809 (mmm) cc_final: -0.2145 (ttm) REVERT: C 77 THR cc_start: 0.1188 (OUTLIER) cc_final: 0.0548 (m) REVERT: C 108 MET cc_start: 0.2728 (mpp) cc_final: -0.0451 (mmt) REVERT: C 111 VAL cc_start: 0.4654 (OUTLIER) cc_final: 0.4430 (p) REVERT: E 873 TYR cc_start: 0.7670 (m-80) cc_final: 0.7280 (m-80) REVERT: E 902 MET cc_start: 0.6503 (mmm) cc_final: 0.6201 (mmm) REVERT: F 2 MET cc_start: 0.0765 (ptt) cc_final: -0.0185 (mpp) REVERT: F 80 MET cc_start: 0.1742 (ppp) cc_final: -0.0035 (tmm) REVERT: F 101 ASP cc_start: 0.5655 (m-30) cc_final: 0.4949 (t0) REVERT: G 392 PHE cc_start: 0.5809 (m-80) cc_final: 0.5408 (m-10) REVERT: G 742 ILE cc_start: 0.9040 (mt) cc_final: 0.8827 (mt) REVERT: G 902 MET cc_start: 0.7773 (mmm) cc_final: 0.7424 (mmm) REVERT: G 904 TYR cc_start: 0.6628 (m-10) cc_final: 0.6374 (m-10) REVERT: G 1047 TYR cc_start: 0.8147 (m-80) cc_final: 0.7899 (m-10) outliers start: 46 outliers final: 27 residues processed: 244 average time/residue: 0.3371 time to fit residues: 139.2848 Evaluate side-chains 213 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 183 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain E residue 200 TYR Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 538 CYS Chi-restraints excluded: chain G residue 200 TYR Chi-restraints excluded: chain G residue 207 HIS Chi-restraints excluded: chain G residue 317 ASN Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 1096 VAL Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 7.9990 chunk 199 optimal weight: 0.3980 chunk 5 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 299 optimal weight: 0.9990 chunk 242 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 179 optimal weight: 0.9990 chunk 314 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN G 207 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27057 Z= 0.219 Angle : 0.523 10.068 36981 Z= 0.267 Chirality : 0.045 0.280 4275 Planarity : 0.004 0.054 4848 Dihedral : 3.609 17.760 3900 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.98 % Allowed : 12.19 % Favored : 85.82 % 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: 0.75 (0.14), residues: 3627 helix: 2.29 (0.20), residues: 678 sheet: 1.00 (0.18), residues: 843 loop : -0.31 (0.14), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 50 HIS 0.011 0.001 HIS G 207 PHE 0.026 0.001 PHE E 168 TYR 0.015 0.001 TYR E1067 ARG 0.004 0.000 ARG G 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 193 time to evaluate : 3.001 Fit side-chains revert: symmetry clash REVERT: A 577 ARG cc_start: 0.7462 (ttm-80) cc_final: 0.7204 (ttm-80) REVERT: A 699 LEU cc_start: 0.8662 (mt) cc_final: 0.8285 (mt) REVERT: A 906 PHE cc_start: 0.8399 (OUTLIER) cc_final: 0.6860 (m-10) REVERT: C 2 MET cc_start: 0.4750 (mmt) cc_final: 0.3981 (mmt) REVERT: C 73 MET cc_start: 0.0866 (mmm) cc_final: -0.2210 (ttm) REVERT: C 77 THR cc_start: 0.1129 (OUTLIER) cc_final: 0.0557 (m) REVERT: C 108 MET cc_start: 0.3546 (mpp) cc_final: -0.0352 (mmt) REVERT: C 111 VAL cc_start: 0.4661 (OUTLIER) cc_final: 0.4452 (p) REVERT: E 571 ASP cc_start: 0.7098 (t0) cc_final: 0.6892 (t70) REVERT: E 873 TYR cc_start: 0.7726 (m-10) cc_final: 0.7350 (m-80) REVERT: E 902 MET cc_start: 0.6834 (mmm) cc_final: 0.6564 (mmm) REVERT: F 2 MET cc_start: 0.0769 (ptt) cc_final: -0.0197 (mpp) REVERT: F 80 MET cc_start: 0.1836 (ppp) cc_final: 0.0115 (tmm) REVERT: G 392 PHE cc_start: 0.5666 (m-80) cc_final: 0.5413 (m-10) REVERT: G 724 THR cc_start: 0.8427 (m) cc_final: 0.8212 (p) REVERT: G 742 ILE cc_start: 0.8979 (mt) cc_final: 0.8766 (mt) REVERT: G 902 MET cc_start: 0.7941 (mmm) cc_final: 0.7581 (mmm) REVERT: G 1047 TYR cc_start: 0.8051 (m-80) cc_final: 0.7794 (m-10) outliers start: 49 outliers final: 30 residues processed: 231 average time/residue: 0.3358 time to fit residues: 131.4125 Evaluate side-chains 212 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 179 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 538 CYS Chi-restraints excluded: chain E residue 759 PHE Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain G residue 200 TYR Chi-restraints excluded: chain G residue 207 HIS Chi-restraints excluded: chain G residue 317 ASN Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 206 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 351 optimal weight: 7.9990 chunk 291 optimal weight: 0.8980 chunk 162 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 116 optimal weight: 0.8980 chunk 184 optimal weight: 0.0870 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 901 GLN G 207 HIS ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27057 Z= 0.175 Angle : 0.508 10.278 36981 Z= 0.256 Chirality : 0.044 0.169 4275 Planarity : 0.004 0.049 4848 Dihedral : 3.521 17.043 3900 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.07 % Allowed : 12.47 % Favored : 85.46 % 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: 0.80 (0.14), residues: 3627 helix: 2.34 (0.20), residues: 678 sheet: 0.99 (0.18), residues: 858 loop : -0.26 (0.14), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 50 HIS 0.008 0.001 HIS G 207 PHE 0.016 0.001 PHE A 92 TYR 0.020 0.001 TYR G 904 ARG 0.003 0.000 ARG G 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 201 time to evaluate : 2.998 Fit side-chains revert: symmetry clash REVERT: A 577 ARG cc_start: 0.7448 (ttm-80) cc_final: 0.7168 (ttm-80) REVERT: A 699 LEU cc_start: 0.8681 (mt) cc_final: 0.8435 (mt) REVERT: A 906 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.6859 (m-10) REVERT: A 970 PHE cc_start: 0.8413 (m-80) cc_final: 0.7936 (m-10) REVERT: C 2 MET cc_start: 0.4730 (mmt) cc_final: 0.3984 (mmt) REVERT: C 73 MET cc_start: 0.1120 (mmm) cc_final: -0.2127 (ttm) REVERT: C 108 MET cc_start: 0.3574 (mpp) cc_final: -0.0315 (mmt) REVERT: C 111 VAL cc_start: 0.4713 (OUTLIER) cc_final: 0.4499 (p) REVERT: E 571 ASP cc_start: 0.7038 (t0) cc_final: 0.6824 (t70) REVERT: E 902 MET cc_start: 0.6860 (mmm) cc_final: 0.6631 (mmm) REVERT: E 904 TYR cc_start: 0.7336 (m-10) cc_final: 0.7117 (m-10) REVERT: E 1134 ASN cc_start: 0.7218 (OUTLIER) cc_final: 0.6746 (m-40) REVERT: F 2 MET cc_start: 0.0772 (ptt) cc_final: -0.0171 (mpp) REVERT: G 117 LEU cc_start: 0.7888 (tp) cc_final: 0.7435 (mt) REVERT: G 392 PHE cc_start: 0.5504 (m-80) cc_final: 0.5275 (m-10) REVERT: G 724 THR cc_start: 0.8454 (m) cc_final: 0.8223 (p) REVERT: G 902 MET cc_start: 0.7839 (mmm) cc_final: 0.7430 (mmm) REVERT: G 1047 TYR cc_start: 0.8038 (m-80) cc_final: 0.7784 (m-10) outliers start: 51 outliers final: 34 residues processed: 239 average time/residue: 0.3450 time to fit residues: 138.5111 Evaluate side-chains 218 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 181 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain E residue 200 TYR Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 538 CYS Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 200 TYR Chi-restraints excluded: chain G residue 207 HIS Chi-restraints excluded: chain G residue 317 ASN Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 869 MET Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 1096 VAL Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 200 optimal weight: 4.9990 chunk 256 optimal weight: 20.0000 chunk 198 optimal weight: 0.0470 chunk 295 optimal weight: 5.9990 chunk 196 optimal weight: 0.8980 chunk 349 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 chunk 213 optimal weight: 6.9990 chunk 161 optimal weight: 0.9980 overall best weight: 1.2058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 HIS ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27057 Z= 0.215 Angle : 0.528 10.397 36981 Z= 0.267 Chirality : 0.045 0.306 4275 Planarity : 0.004 0.058 4848 Dihedral : 3.562 16.552 3900 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.23 % Allowed : 12.84 % Favored : 84.93 % 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: 3627 helix: 2.12 (0.20), residues: 696 sheet: 0.99 (0.18), residues: 858 loop : -0.26 (0.14), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 50 HIS 0.003 0.001 HIS E1064 PHE 0.032 0.002 PHE G 168 TYR 0.024 0.001 TYR G 904 ARG 0.007 0.000 ARG G 815 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 194 time to evaluate : 3.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 241 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6683 (mm) REVERT: A 699 LEU cc_start: 0.8598 (mt) cc_final: 0.8357 (mt) REVERT: A 906 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.6897 (m-10) REVERT: C 2 MET cc_start: 0.5085 (mmt) cc_final: 0.4185 (mmt) REVERT: C 46 GLU cc_start: 0.0915 (OUTLIER) cc_final: -0.0208 (pp20) REVERT: C 50 TRP cc_start: 0.6009 (p-90) cc_final: 0.5561 (p90) REVERT: C 65 GLU cc_start: 0.2030 (OUTLIER) cc_final: 0.1782 (pp20) REVERT: C 73 MET cc_start: 0.1092 (mmm) cc_final: -0.2255 (ttp) REVERT: C 108 MET cc_start: 0.3614 (mpp) cc_final: -0.0281 (mmt) REVERT: C 111 VAL cc_start: 0.4763 (OUTLIER) cc_final: 0.4523 (p) REVERT: E 571 ASP cc_start: 0.7119 (t0) cc_final: 0.6900 (t70) REVERT: E 902 MET cc_start: 0.6977 (mmm) cc_final: 0.6728 (mmm) REVERT: E 904 TYR cc_start: 0.7405 (m-10) cc_final: 0.7167 (m-10) REVERT: E 994 ASP cc_start: 0.7867 (t70) cc_final: 0.7601 (t0) REVERT: E 1134 ASN cc_start: 0.7785 (OUTLIER) cc_final: 0.7347 (m-40) REVERT: F 46 GLU cc_start: 0.0493 (OUTLIER) cc_final: -0.0654 (pm20) REVERT: F 80 MET cc_start: 0.2924 (ppp) cc_final: -0.0410 (tmm) REVERT: G 392 PHE cc_start: 0.5574 (m-80) cc_final: 0.5372 (m-80) REVERT: G 724 THR cc_start: 0.8485 (m) cc_final: 0.8244 (p) REVERT: G 902 MET cc_start: 0.7918 (mmm) cc_final: 0.7501 (mmm) REVERT: G 1047 TYR cc_start: 0.8073 (m-80) cc_final: 0.7847 (m-10) outliers start: 55 outliers final: 35 residues processed: 237 average time/residue: 0.3764 time to fit residues: 149.1951 Evaluate side-chains 220 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 178 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 538 CYS Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 200 TYR Chi-restraints excluded: chain G residue 207 HIS Chi-restraints excluded: chain G residue 317 ASN Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 869 MET Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 0.7980 chunk 139 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 105 optimal weight: 0.2980 chunk 68 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 238 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 32 optimal weight: 30.0000 chunk 275 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 HIS ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27057 Z= 0.160 Angle : 0.517 10.537 36981 Z= 0.259 Chirality : 0.045 0.286 4275 Planarity : 0.004 0.051 4848 Dihedral : 3.487 16.115 3900 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.94 % Allowed : 13.57 % Favored : 84.49 % 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: 0.79 (0.14), residues: 3627 helix: 2.15 (0.20), residues: 696 sheet: 1.02 (0.18), residues: 864 loop : -0.25 (0.14), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 50 HIS 0.008 0.001 HIS G 207 PHE 0.023 0.001 PHE G 275 TYR 0.031 0.001 TYR G 904 ARG 0.004 0.000 ARG G 815 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 3.011 Fit side-chains REVERT: A 131 CYS cc_start: -0.0109 (m) cc_final: -0.0766 (m) REVERT: A 699 LEU cc_start: 0.8664 (mt) cc_final: 0.8464 (mt) REVERT: A 906 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.6841 (m-10) REVERT: C 2 MET cc_start: 0.4984 (mmt) cc_final: 0.4055 (mmt) REVERT: C 46 GLU cc_start: 0.0687 (OUTLIER) cc_final: -0.0353 (pp20) REVERT: C 50 TRP cc_start: 0.5989 (p-90) cc_final: 0.5611 (p90) REVERT: C 65 GLU cc_start: 0.2058 (OUTLIER) cc_final: 0.1770 (pp20) REVERT: C 73 MET cc_start: 0.1148 (mmm) cc_final: -0.1934 (ttp) REVERT: C 108 MET cc_start: 0.3629 (mpp) cc_final: -0.0253 (mmt) REVERT: C 111 VAL cc_start: 0.4751 (OUTLIER) cc_final: 0.4512 (p) REVERT: E 571 ASP cc_start: 0.7138 (t0) cc_final: 0.6913 (t70) REVERT: E 675 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7602 (pp30) REVERT: E 1134 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7335 (m-40) REVERT: F 46 GLU cc_start: 0.0241 (OUTLIER) cc_final: -0.0574 (pm20) REVERT: F 80 MET cc_start: 0.2932 (ppp) cc_final: -0.0485 (tmm) REVERT: G 724 THR cc_start: 0.8481 (m) cc_final: 0.8230 (p) REVERT: G 902 MET cc_start: 0.7778 (mmm) cc_final: 0.7340 (mmm) REVERT: G 1047 TYR cc_start: 0.8067 (m-80) cc_final: 0.7857 (m-10) outliers start: 48 outliers final: 32 residues processed: 225 average time/residue: 0.3388 time to fit residues: 130.1461 Evaluate side-chains 215 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 176 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 65 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 538 CYS Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 200 TYR Chi-restraints excluded: chain G residue 317 ASN Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 869 MET Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 1.9990 chunk 335 optimal weight: 2.9990 chunk 305 optimal weight: 5.9990 chunk 326 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 256 optimal weight: 3.9990 chunk 100 optimal weight: 0.1980 chunk 294 optimal weight: 0.8980 chunk 308 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN G 907 ASN ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 27057 Z= 0.243 Angle : 0.550 11.219 36981 Z= 0.277 Chirality : 0.045 0.272 4275 Planarity : 0.004 0.050 4848 Dihedral : 3.628 16.041 3900 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.86 % Allowed : 14.22 % Favored : 83.92 % 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: 0.68 (0.14), residues: 3627 helix: 2.21 (0.20), residues: 675 sheet: 0.88 (0.17), residues: 924 loop : -0.34 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 50 HIS 0.008 0.001 HIS E1064 PHE 0.025 0.002 PHE E 168 TYR 0.049 0.001 TYR G 904 ARG 0.005 0.000 ARG E1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 183 time to evaluate : 3.085 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: -0.0032 (m) cc_final: -0.0718 (m) REVERT: A 275 PHE cc_start: 0.7593 (m-80) cc_final: 0.7199 (m-10) REVERT: A 699 LEU cc_start: 0.8647 (mt) cc_final: 0.8402 (mt) REVERT: C 2 MET cc_start: 0.5918 (mmt) cc_final: 0.4804 (mmt) REVERT: C 46 GLU cc_start: 0.0892 (OUTLIER) cc_final: -0.0253 (pp20) REVERT: C 73 MET cc_start: 0.1322 (mmm) cc_final: -0.2104 (ttp) REVERT: C 108 MET cc_start: 0.3673 (mpp) cc_final: -0.0218 (mmt) REVERT: C 111 VAL cc_start: 0.5069 (OUTLIER) cc_final: 0.4865 (p) REVERT: E 675 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7461 (pp30) REVERT: E 1134 ASN cc_start: 0.7789 (OUTLIER) cc_final: 0.7358 (m-40) REVERT: F 46 GLU cc_start: 0.0272 (OUTLIER) cc_final: -0.0583 (pm20) REVERT: F 80 MET cc_start: 0.2901 (ppp) cc_final: -0.0303 (tmm) REVERT: G 117 LEU cc_start: 0.7898 (tp) cc_final: 0.7495 (mp) REVERT: G 724 THR cc_start: 0.8528 (m) cc_final: 0.8277 (p) REVERT: G 902 MET cc_start: 0.8015 (mmm) cc_final: 0.7548 (mmm) REVERT: G 998 THR cc_start: 0.8623 (m) cc_final: 0.8322 (p) REVERT: G 1047 TYR cc_start: 0.8059 (m-80) cc_final: 0.7813 (m-10) outliers start: 46 outliers final: 33 residues processed: 222 average time/residue: 0.3353 time to fit residues: 127.4759 Evaluate side-chains 216 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 178 time to evaluate : 3.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 538 CYS Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 808 ASP Chi-restraints excluded: chain E residue 873 TYR Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 50 TRP Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 317 ASN Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 869 MET Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain I residue 59 TYR Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 5.9990 chunk 344 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 239 optimal weight: 1.9990 chunk 361 optimal weight: 9.9990 chunk 332 optimal weight: 0.9990 chunk 287 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 222 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 901 GLN G 907 ASN ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27057 Z= 0.267 Angle : 0.565 11.417 36981 Z= 0.287 Chirality : 0.046 0.266 4275 Planarity : 0.004 0.054 4848 Dihedral : 3.753 16.562 3900 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.62 % Allowed : 14.38 % Favored : 84.00 % 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: 3627 helix: 2.13 (0.20), residues: 672 sheet: 0.74 (0.17), residues: 972 loop : -0.40 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 50 HIS 0.002 0.001 HIS G1088 PHE 0.028 0.002 PHE A 592 TYR 0.054 0.001 TYR E 904 ARG 0.007 0.000 ARG A1107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 2.939 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: 0.0055 (m) cc_final: -0.0617 (m) REVERT: A 275 PHE cc_start: 0.7188 (m-80) cc_final: 0.6973 (m-10) REVERT: A 377 PHE cc_start: 0.3766 (t80) cc_final: 0.3510 (t80) REVERT: A 699 LEU cc_start: 0.8672 (mt) cc_final: 0.8433 (mt) REVERT: C 2 MET cc_start: 0.5791 (mmt) cc_final: 0.4817 (mmt) REVERT: C 46 GLU cc_start: 0.0631 (OUTLIER) cc_final: -0.0443 (pp20) REVERT: C 73 MET cc_start: 0.1606 (mmm) cc_final: -0.2026 (ttp) REVERT: C 108 MET cc_start: 0.3328 (mpp) cc_final: 0.0301 (mmt) REVERT: E 675 GLN cc_start: 0.8030 (OUTLIER) cc_final: 0.7688 (pp30) REVERT: E 1134 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7301 (m-40) REVERT: F 46 GLU cc_start: 0.0311 (OUTLIER) cc_final: -0.0605 (pm20) REVERT: F 80 MET cc_start: 0.2819 (ppp) cc_final: -0.0458 (tmm) REVERT: G 117 LEU cc_start: 0.7884 (tp) cc_final: 0.7495 (mp) REVERT: G 237 ARG cc_start: 0.7185 (ptt-90) cc_final: 0.6976 (ptt90) REVERT: G 902 MET cc_start: 0.7978 (mmm) cc_final: 0.7487 (mmm) REVERT: G 998 THR cc_start: 0.8706 (m) cc_final: 0.8385 (p) REVERT: G 1047 TYR cc_start: 0.8077 (m-80) cc_final: 0.7840 (m-10) outliers start: 40 outliers final: 30 residues processed: 216 average time/residue: 0.3252 time to fit residues: 121.6776 Evaluate side-chains 209 residues out of total 3201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 310 LYS Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain E residue 317 ASN Chi-restraints excluded: chain E residue 538 CYS Chi-restraints excluded: chain E residue 675 GLN Chi-restraints excluded: chain E residue 763 LEU Chi-restraints excluded: chain E residue 775 ASP Chi-restraints excluded: chain E residue 1104 VAL Chi-restraints excluded: chain E residue 1134 ASN Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 317 ASN Chi-restraints excluded: chain G residue 538 CYS Chi-restraints excluded: chain G residue 560 LEU Chi-restraints excluded: chain G residue 721 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 869 MET Chi-restraints excluded: chain G residue 900 MET Chi-restraints excluded: chain G residue 907 ASN Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 0.8980 chunk 306 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 265 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 288 optimal weight: 7.9990 chunk 120 optimal weight: 0.0670 chunk 296 optimal weight: 0.1980 chunk 36 optimal weight: 50.0000 chunk 53 optimal weight: 0.0670 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.179756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.119038 restraints weight = 52283.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.121734 restraints weight = 33027.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.122338 restraints weight = 17906.308| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27057 Z= 0.139 Angle : 0.530 11.612 36981 Z= 0.263 Chirality : 0.045 0.271 4275 Planarity : 0.004 0.053 4848 Dihedral : 3.494 15.550 3900 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.13 % Allowed : 15.07 % Favored : 83.80 % 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: 0.75 (0.14), residues: 3627 helix: 2.32 (0.20), residues: 675 sheet: 0.83 (0.17), residues: 954 loop : -0.28 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 50 HIS 0.001 0.000 HIS A 66 PHE 0.025 0.001 PHE E 168 TYR 0.035 0.001 TYR G 904 ARG 0.004 0.000 ARG G 905 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4486.69 seconds wall clock time: 83 minutes 20.47 seconds (5000.47 seconds total)