Starting phenix.real_space_refine on Mon Sep 30 10:13:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxo_25502/09_2024/7sxo_25502.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxo_25502/09_2024/7sxo_25502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxo_25502/09_2024/7sxo_25502.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxo_25502/09_2024/7sxo_25502.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxo_25502/09_2024/7sxo_25502.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sxo_25502/09_2024/7sxo_25502.cif" } resolution = 3.3 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= 0.001 sd= 0.051 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 4 5.21 5 S 108 5.16 5 C 15849 2.51 5 N 4216 2.21 5 O 4701 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24894 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4256 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 516} Chain breaks: 3 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3793 Classifications: {'peptide': 487} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 461} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "C" Number of atoms: 3786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3786 Classifications: {'peptide': 487} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 25, 'TRANS': 461} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 4262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4262 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 27, 'TRANS': 519} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 4278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4278 Classifications: {'peptide': 546} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 518} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4292 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 27, 'TRANS': 521} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 45 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'UNK:plan-1': 9} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.25, per 1000 atoms: 0.61 Number of scatterers: 24894 At special positions: 0 Unit cell: (131.1, 136.85, 141.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 16 15.00 Mg 4 11.99 O 4701 8.00 N 4216 7.00 C 15849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 629 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B 629 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS D 629 " - pdb=" SG CYS D 747 " distance=2.04 Simple disulfide: pdb=" SG CYS F 629 " - pdb=" SG CYS F 747 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.96 Conformation dependent library (CDL) restraints added in 3.2 seconds 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5890 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 30 sheets defined 47.6% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 530 through 538 removed outlier: 3.558A pdb=" N ILE A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 556 Processing helix chain 'A' and resid 561 through 577 removed outlier: 4.307A pdb=" N GLY A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 600 removed outlier: 4.073A pdb=" N ASP A 599 " --> pdb=" O ILE A 595 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 619 Processing helix chain 'A' and resid 640 through 649 removed outlier: 4.177A pdb=" N SER A 644 " --> pdb=" O SER A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 680 through 690 Processing helix chain 'A' and resid 712 through 722 removed outlier: 3.675A pdb=" N ALA A 716 " --> pdb=" O ASP A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 729 removed outlier: 3.990A pdb=" N PHE A 729 " --> pdb=" O ASN A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 763 Processing helix chain 'A' and resid 772 through 792 removed outlier: 5.327A pdb=" N VAL A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) Proline residue: A 786 - end of helix Processing helix chain 'A' and resid 802 through 813 Processing helix chain 'A' and resid 819 through 840 removed outlier: 3.615A pdb=" N LYS A 840 " --> pdb=" O GLN A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 966 through 989 removed outlier: 4.165A pdb=" N MET A 970 " --> pdb=" O LEU A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1016 through 1030 removed outlier: 3.595A pdb=" N ALA A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1065 Processing helix chain 'A' and resid 1076 through 1083 Processing helix chain 'A' and resid 1084 through 1089 Processing helix chain 'A' and resid 1098 through 1107 removed outlier: 4.067A pdb=" N ILE A1102 " --> pdb=" O TRP A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1129 removed outlier: 3.850A pdb=" N ILE A1125 " --> pdb=" O ALA A1121 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU A1126 " --> pdb=" O GLU A1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 600 removed outlier: 3.747A pdb=" N GLU B 598 " --> pdb=" O LYS B 594 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP B 599 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N HIS B 600 " --> pdb=" O LEU B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 603 through 620 removed outlier: 3.969A pdb=" N LYS B 607 " --> pdb=" O MET B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 650 removed outlier: 4.432A pdb=" N LYS B 643 " --> pdb=" O THR B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 690 removed outlier: 3.594A pdb=" N GLN B 684 " --> pdb=" O GLY B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 722 removed outlier: 4.368A pdb=" N ALA B 716 " --> pdb=" O ASP B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 722 through 727 removed outlier: 4.064A pdb=" N ASN B 727 " --> pdb=" O PRO B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 761 Processing helix chain 'B' and resid 772 through 793 removed outlier: 4.823A pdb=" N VAL B 785 " --> pdb=" O GLU B 781 " (cutoff:3.500A) Proline residue: B 786 - end of helix Processing helix chain 'B' and resid 802 through 813 Processing helix chain 'B' and resid 819 through 841 Processing helix chain 'B' and resid 966 through 989 removed outlier: 4.054A pdb=" N MET B 970 " --> pdb=" O LEU B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 998 removed outlier: 4.187A pdb=" N LYS B 997 " --> pdb=" O ARG B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1015 No H-bonds generated for 'chain 'B' and resid 1013 through 1015' Processing helix chain 'B' and resid 1016 through 1030 removed outlier: 3.640A pdb=" N LEU B1025 " --> pdb=" O ALA B1021 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1065 Processing helix chain 'B' and resid 1076 through 1082 removed outlier: 3.539A pdb=" N GLU B1081 " --> pdb=" O LEU B1077 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU B1082 " --> pdb=" O ASN B1078 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1089 Processing helix chain 'B' and resid 1098 through 1107 removed outlier: 4.087A pdb=" N ILE B1102 " --> pdb=" O TRP B1098 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 600 Processing helix chain 'C' and resid 603 through 619 removed outlier: 3.613A pdb=" N LEU C 619 " --> pdb=" O ALA C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 649 removed outlier: 3.575A pdb=" N SER C 644 " --> pdb=" O SER C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 669 removed outlier: 3.671A pdb=" N GLY C 669 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 690 removed outlier: 4.703A pdb=" N GLN C 690 " --> pdb=" O LEU C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 722 removed outlier: 3.631A pdb=" N ALA C 716 " --> pdb=" O ASP C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 762 removed outlier: 4.069A pdb=" N ARG C 762 " --> pdb=" O PRO C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 792 removed outlier: 5.099A pdb=" N VAL C 785 " --> pdb=" O GLU C 781 " (cutoff:3.500A) Proline residue: C 786 - end of helix Processing helix chain 'C' and resid 802 through 813 Processing helix chain 'C' and resid 819 through 841 Processing helix chain 'C' and resid 951 through 955 Processing helix chain 'C' and resid 966 through 989 removed outlier: 4.152A pdb=" N MET C 970 " --> pdb=" O LEU C 966 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 986 " --> pdb=" O LYS C 982 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 997 Processing helix chain 'C' and resid 1013 through 1015 No H-bonds generated for 'chain 'C' and resid 1013 through 1015' Processing helix chain 'C' and resid 1016 through 1030 removed outlier: 3.610A pdb=" N LEU C1025 " --> pdb=" O ALA C1021 " (cutoff:3.500A) Processing helix chain 'C' and resid 1055 through 1065 Processing helix chain 'C' and resid 1076 through 1083 Processing helix chain 'C' and resid 1084 through 1089 removed outlier: 3.857A pdb=" N LYS C1088 " --> pdb=" O PRO C1084 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU C1089 " --> pdb=" O ASP C1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1084 through 1089' Processing helix chain 'C' and resid 1098 through 1107 removed outlier: 4.222A pdb=" N ILE C1102 " --> pdb=" O TRP C1098 " (cutoff:3.500A) Processing helix chain 'C' and resid 1119 through 1123 Processing helix chain 'D' and resid 530 through 537 removed outlier: 3.753A pdb=" N ILE D 534 " --> pdb=" O TYR D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 556 removed outlier: 4.187A pdb=" N THR D 556 " --> pdb=" O THR D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 561 through 576 removed outlier: 3.798A pdb=" N GLY D 565 " --> pdb=" O MET D 561 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 576 " --> pdb=" O ASP D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 598 removed outlier: 3.501A pdb=" N GLU D 598 " --> pdb=" O LYS D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 620 Processing helix chain 'D' and resid 640 through 649 removed outlier: 3.850A pdb=" N SER D 644 " --> pdb=" O SER D 640 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 669 Processing helix chain 'D' and resid 680 through 690 Processing helix chain 'D' and resid 712 through 722 removed outlier: 3.889A pdb=" N ALA D 716 " --> pdb=" O ASP D 712 " (cutoff:3.500A) Processing helix chain 'D' and resid 724 through 729 removed outlier: 3.821A pdb=" N ASN D 727 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE D 729 " --> pdb=" O ASN D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 762 removed outlier: 3.866A pdb=" N ARG D 762 " --> pdb=" O PRO D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 792 removed outlier: 4.798A pdb=" N VAL D 785 " --> pdb=" O GLU D 781 " (cutoff:3.500A) Proline residue: D 786 - end of helix Processing helix chain 'D' and resid 802 through 814 removed outlier: 3.617A pdb=" N CYS D 814 " --> pdb=" O MET D 810 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 839 Processing helix chain 'D' and resid 905 through 909 removed outlier: 3.766A pdb=" N ASP D 908 " --> pdb=" O ASN D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 989 removed outlier: 4.161A pdb=" N MET D 970 " --> pdb=" O LEU D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 993 through 997 Processing helix chain 'D' and resid 1013 through 1015 No H-bonds generated for 'chain 'D' and resid 1013 through 1015' Processing helix chain 'D' and resid 1016 through 1029 removed outlier: 3.504A pdb=" N LEU D1025 " --> pdb=" O ALA D1021 " (cutoff:3.500A) Processing helix chain 'D' and resid 1055 through 1065 Processing helix chain 'D' and resid 1076 through 1082 Processing helix chain 'D' and resid 1084 through 1089 Processing helix chain 'D' and resid 1098 through 1107 removed outlier: 4.073A pdb=" N ILE D1102 " --> pdb=" O TRP D1098 " (cutoff:3.500A) Processing helix chain 'D' and resid 1119 through 1125 Processing helix chain 'E' and resid 530 through 538 removed outlier: 3.585A pdb=" N ILE E 534 " --> pdb=" O TYR E 530 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS E 538 " --> pdb=" O ILE E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 556 removed outlier: 3.720A pdb=" N THR E 556 " --> pdb=" O THR E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 561 through 577 removed outlier: 4.160A pdb=" N GLY E 565 " --> pdb=" O MET E 561 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE E 577 " --> pdb=" O TRP E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 598 Processing helix chain 'E' and resid 603 through 621 removed outlier: 3.595A pdb=" N LEU E 620 " --> pdb=" O VAL E 616 " (cutoff:3.500A) Processing helix chain 'E' and resid 640 through 649 removed outlier: 3.898A pdb=" N SER E 644 " --> pdb=" O SER E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 669 Processing helix chain 'E' and resid 680 through 690 Processing helix chain 'E' and resid 712 through 721 removed outlier: 3.884A pdb=" N ALA E 716 " --> pdb=" O ASP E 712 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 729 removed outlier: 4.199A pdb=" N PHE E 729 " --> pdb=" O ASN E 726 " (cutoff:3.500A) Processing helix chain 'E' and resid 756 through 762 removed outlier: 3.773A pdb=" N ARG E 762 " --> pdb=" O PRO E 758 " (cutoff:3.500A) Processing helix chain 'E' and resid 772 through 792 removed outlier: 5.221A pdb=" N VAL E 785 " --> pdb=" O GLU E 781 " (cutoff:3.500A) Proline residue: E 786 - end of helix Processing helix chain 'E' and resid 802 through 813 Processing helix chain 'E' and resid 819 through 841 Processing helix chain 'E' and resid 902 through 905 Processing helix chain 'E' and resid 906 through 911 Processing helix chain 'E' and resid 951 through 955 removed outlier: 3.560A pdb=" N CYS E 955 " --> pdb=" O LEU E 952 " (cutoff:3.500A) Processing helix chain 'E' and resid 966 through 989 removed outlier: 4.088A pdb=" N MET E 970 " --> pdb=" O LEU E 966 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 986 " --> pdb=" O LYS E 982 " (cutoff:3.500A) Processing helix chain 'E' and resid 993 through 997 removed outlier: 3.583A pdb=" N LYS E 997 " --> pdb=" O PHE E 994 " (cutoff:3.500A) Processing helix chain 'E' and resid 1013 through 1015 No H-bonds generated for 'chain 'E' and resid 1013 through 1015' Processing helix chain 'E' and resid 1016 through 1030 removed outlier: 3.540A pdb=" N LEU E1029 " --> pdb=" O LEU E1025 " (cutoff:3.500A) Processing helix chain 'E' and resid 1055 through 1065 Processing helix chain 'E' and resid 1076 through 1082 Processing helix chain 'E' and resid 1084 through 1089 removed outlier: 3.966A pdb=" N LYS E1088 " --> pdb=" O PRO E1084 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU E1089 " --> pdb=" O ASP E1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1084 through 1089' Processing helix chain 'E' and resid 1098 through 1107 removed outlier: 4.103A pdb=" N ILE E1102 " --> pdb=" O TRP E1098 " (cutoff:3.500A) Processing helix chain 'E' and resid 1120 through 1127 removed outlier: 3.651A pdb=" N ILE E1125 " --> pdb=" O ALA E1121 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 536 Processing helix chain 'F' and resid 540 through 556 removed outlier: 3.752A pdb=" N THR F 556 " --> pdb=" O THR F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 577 removed outlier: 4.219A pdb=" N GLY F 565 " --> pdb=" O MET F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 598 Processing helix chain 'F' and resid 603 through 619 removed outlier: 3.533A pdb=" N LEU F 619 " --> pdb=" O ALA F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 649 removed outlier: 4.300A pdb=" N SER F 644 " --> pdb=" O SER F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 663 through 667 Processing helix chain 'F' and resid 680 through 690 Processing helix chain 'F' and resid 712 through 721 Processing helix chain 'F' and resid 756 through 762 removed outlier: 3.854A pdb=" N ARG F 762 " --> pdb=" O PRO F 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 772 through 791 removed outlier: 5.370A pdb=" N VAL F 785 " --> pdb=" O GLU F 781 " (cutoff:3.500A) Proline residue: F 786 - end of helix Processing helix chain 'F' and resid 802 through 813 Processing helix chain 'F' and resid 819 through 841 Processing helix chain 'F' and resid 902 through 906 Processing helix chain 'F' and resid 967 through 989 removed outlier: 3.501A pdb=" N SER F 979 " --> pdb=" O ARG F 975 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA F 986 " --> pdb=" O LYS F 982 " (cutoff:3.500A) Processing helix chain 'F' and resid 1019 through 1029 removed outlier: 3.644A pdb=" N LEU F1025 " --> pdb=" O ALA F1021 " (cutoff:3.500A) Processing helix chain 'F' and resid 1054 through 1065 removed outlier: 3.536A pdb=" N LYS F1058 " --> pdb=" O GLY F1054 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA F1061 " --> pdb=" O GLU F1057 " (cutoff:3.500A) Processing helix chain 'F' and resid 1076 through 1083 Processing helix chain 'F' and resid 1084 through 1089 Processing helix chain 'F' and resid 1098 through 1107 removed outlier: 4.129A pdb=" N ILE F1102 " --> pdb=" O TRP F1098 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 653 through 656 removed outlier: 6.476A pdb=" N ILE A 628 " --> pdb=" O CYS A 747 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ALA A 749 " --> pdb=" O ILE A 628 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE A 630 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 627 " --> pdb=" O GLU A 764 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE A 766 " --> pdb=" O ILE A 627 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS A 629 " --> pdb=" O ILE A 766 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 799 through 801 removed outlier: 6.459A pdb=" N ASP A 800 " --> pdb=" O ILE A 901 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 928 through 935 removed outlier: 6.587A pdb=" N GLU A 961 " --> pdb=" O LEU A1002 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1037 through 1039 removed outlier: 6.706A pdb=" N ILE A1070 " --> pdb=" O LEU A1094 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALA A1096 " --> pdb=" O ILE A1070 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N PHE A1072 " --> pdb=" O ALA A1096 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1042 through 1043 removed outlier: 3.584A pdb=" N GLU A1042 " --> pdb=" O LEU A1050 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 628 through 631 removed outlier: 4.068A pdb=" N ILE B 628 " --> pdb=" O PHE B 745 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE B 696 " --> pdb=" O VAL B 746 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N THR B 748 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE B 698 " --> pdb=" O THR B 748 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 799 through 801 removed outlier: 6.829A pdb=" N ASP B 800 " --> pdb=" O ILE B 901 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 928 through 935 removed outlier: 6.185A pdb=" N THR B 959 " --> pdb=" O ILE B1000 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LEU B1002 " --> pdb=" O THR B 959 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLU B 961 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1069 through 1073 removed outlier: 7.222A pdb=" N ILE B1070 " --> pdb=" O LEU B1094 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ALA B1096 " --> pdb=" O ILE B1070 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE B1072 " --> pdb=" O ALA B1096 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 629 through 631 Processing sheet with id=AB2, first strand: chain 'C' and resid 654 through 656 removed outlier: 7.083A pdb=" N PHE C 654 " --> pdb=" O LEU C 697 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 799 through 801 removed outlier: 7.204A pdb=" N ASP C 800 " --> pdb=" O ILE C 901 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 928 through 934 removed outlier: 6.564A pdb=" N GLU C 961 " --> pdb=" O LEU C1002 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1037 through 1039 Processing sheet with id=AB6, first strand: chain 'C' and resid 1042 through 1043 removed outlier: 3.667A pdb=" N GLU C1042 " --> pdb=" O LEU C1050 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 653 through 656 removed outlier: 6.684A pdb=" N PHE D 654 " --> pdb=" O LEU D 697 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE D 628 " --> pdb=" O CYS D 747 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ALA D 749 " --> pdb=" O ILE D 628 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N PHE D 630 " --> pdb=" O ALA D 749 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 799 through 801 removed outlier: 7.079A pdb=" N ASP D 800 " --> pdb=" O ILE D 901 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 928 through 935 Processing sheet with id=AC1, first strand: chain 'D' and resid 1037 through 1039 removed outlier: 7.469A pdb=" N ALA D1096 " --> pdb=" O ILE D1070 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N PHE D1072 " --> pdb=" O ALA D1096 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1042 through 1043 removed outlier: 3.803A pdb=" N GLU D1042 " --> pdb=" O LEU D1050 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 653 through 656 removed outlier: 3.541A pdb=" N ILE E 696 " --> pdb=" O LEU E 744 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE E 628 " --> pdb=" O CYS E 747 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA E 749 " --> pdb=" O ILE E 628 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE E 630 " --> pdb=" O ALA E 749 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 799 through 800 removed outlier: 3.504A pdb=" N ASP E 800 " --> pdb=" O VAL E 899 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 928 through 930 removed outlier: 6.519A pdb=" N THR E 959 " --> pdb=" O ILE E1000 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU E1002 " --> pdb=" O THR E 959 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU E 961 " --> pdb=" O LEU E1002 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 933 through 934 Processing sheet with id=AC7, first strand: chain 'E' and resid 1037 through 1039 removed outlier: 6.759A pdb=" N ILE E1070 " --> pdb=" O LEU E1094 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ALA E1096 " --> pdb=" O ILE E1070 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N PHE E1072 " --> pdb=" O ALA E1096 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 1042 through 1043 removed outlier: 3.755A pdb=" N GLU E1042 " --> pdb=" O LEU E1050 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 653 through 656 removed outlier: 6.751A pdb=" N ILE F 627 " --> pdb=" O GLU F 764 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE F 766 " --> pdb=" O ILE F 627 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS F 629 " --> pdb=" O ILE F 766 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 800 through 801 removed outlier: 6.614A pdb=" N ASP F 800 " --> pdb=" O ILE F 901 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 928 through 934 removed outlier: 6.429A pdb=" N GLU F 961 " --> pdb=" O LEU F1002 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 1037 through 1039 removed outlier: 6.761A pdb=" N ALA F1038 " --> pdb=" O ILE F1071 " (cutoff:3.500A) 1016 hydrogen bonds defined for protein. 2970 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: 7.69 Time building geometry restraints manager: 6.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4633 1.33 - 1.45: 6219 1.45 - 1.58: 14325 1.58 - 1.71: 22 1.71 - 1.84: 178 Bond restraints: 25377 Sorted by residual: bond pdb=" C LEU F 920 " pdb=" N TYR F 921 " ideal model delta sigma weight residual 1.331 1.243 0.088 1.33e-02 5.65e+03 4.40e+01 bond pdb=" C LYS C1120 " pdb=" O LYS C1120 " ideal model delta sigma weight residual 1.235 1.199 0.036 1.26e-02 6.30e+03 8.33e+00 bond pdb=" C PRO F 912 " pdb=" N PRO F 913 " ideal model delta sigma weight residual 1.331 1.363 -0.032 1.27e-02 6.20e+03 6.38e+00 bond pdb=" CA LYS C1120 " pdb=" CB LYS C1120 " ideal model delta sigma weight residual 1.530 1.511 0.019 1.69e-02 3.50e+03 1.25e+00 bond pdb=" CB ASN D 693 " pdb=" CG ASN D 693 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 1.02e+00 ... (remaining 25372 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.34: 34321 7.34 - 14.69: 8 14.69 - 22.03: 0 22.03 - 29.37: 1 29.37 - 36.72: 1 Bond angle restraints: 34331 Sorted by residual: angle pdb=" N LEU F 920 " pdb=" CA LEU F 920 " pdb=" C LEU F 920 " ideal model delta sigma weight residual 110.91 147.63 -36.72 1.17e+00 7.31e-01 9.85e+02 angle pdb=" C LEU F 920 " pdb=" CA LEU F 920 " pdb=" CB LEU F 920 " ideal model delta sigma weight residual 112.27 84.20 28.07 1.75e+00 3.27e-01 2.57e+02 angle pdb=" N PRO E 958 " pdb=" CA PRO E 958 " pdb=" CB PRO E 958 " ideal model delta sigma weight residual 103.25 111.52 -8.27 1.05e+00 9.07e-01 6.21e+01 angle pdb=" O LEU F 920 " pdb=" C LEU F 920 " pdb=" N TYR F 921 " ideal model delta sigma weight residual 123.33 116.85 6.48 1.22e+00 6.72e-01 2.82e+01 angle pdb=" CA LEU F 920 " pdb=" C LEU F 920 " pdb=" N TYR F 921 " ideal model delta sigma weight residual 114.17 121.44 -7.27 1.45e+00 4.76e-01 2.51e+01 ... (remaining 34326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.88: 14628 24.88 - 49.77: 819 49.77 - 74.65: 77 74.65 - 99.53: 33 99.53 - 124.42: 2 Dihedral angle restraints: 15559 sinusoidal: 6415 harmonic: 9144 Sorted by residual: dihedral pdb=" CB CYS B 629 " pdb=" SG CYS B 629 " pdb=" SG CYS B 747 " pdb=" CB CYS B 747 " ideal model delta sinusoidal sigma weight residual -86.00 -32.71 -53.29 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" O1B ADP B1200 " pdb=" O3A ADP B1200 " pdb=" PB ADP B1200 " pdb=" PA ADP B1200 " ideal model delta sinusoidal sigma weight residual -60.00 64.41 -124.42 1 2.00e+01 2.50e-03 3.76e+01 dihedral pdb=" CB CYS A 629 " pdb=" SG CYS A 629 " pdb=" SG CYS A 747 " pdb=" CB CYS A 747 " ideal model delta sinusoidal sigma weight residual -86.00 -36.24 -49.76 1 1.00e+01 1.00e-02 3.40e+01 ... (remaining 15556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 3887 0.189 - 0.378: 3 0.378 - 0.568: 0 0.568 - 0.757: 0 0.757 - 0.946: 1 Chirality restraints: 3891 Sorted by residual: chirality pdb=" CA LEU F 920 " pdb=" N LEU F 920 " pdb=" C LEU F 920 " pdb=" CB LEU F 920 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.24e+01 chirality pdb=" CA ASN F 954 " pdb=" N ASN F 954 " pdb=" C ASN F 954 " pdb=" CB ASN F 954 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ASN D 693 " pdb=" N ASN D 693 " pdb=" C ASN D 693 " pdb=" CB ASN D 693 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3888 not shown) Planarity restraints: 4343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 757 " -0.055 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO D 758 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 758 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 758 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 678 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO E 679 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 679 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 679 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 912 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO F 913 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO F 913 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 913 " -0.035 5.00e-02 4.00e+02 ... (remaining 4340 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 338 2.65 - 3.22: 23005 3.22 - 3.78: 37793 3.78 - 4.34: 52104 4.34 - 4.90: 85976 Nonbonded interactions: 199216 Sorted by model distance: nonbonded pdb=" O LEU F 920 " pdb=" CB LEU F 920 " model vdw 2.092 2.752 nonbonded pdb=" OD1 ASN D 750 " pdb="MG MG D1201 " model vdw 2.114 2.170 nonbonded pdb=" NH1 ARG C 651 " pdb=" O GLN C 692 " model vdw 2.139 3.120 nonbonded pdb=" OG SER B 946 " pdb=" OH TYR B 978 " model vdw 2.193 3.040 nonbonded pdb=" OG1 THR D1046 " pdb=" OH TYR E 921 " model vdw 2.206 3.040 ... (remaining 199211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 628 or (resid 629 and (name N or name CA or name C \ or name O or name CB )) or resid 630 through 637 or (resid 638 and (name N or na \ me CA or name C or name O or name CB )) or resid 639 through 702 or (resid 703 a \ nd (name N or name CA or name C or name O or name CB )) or resid 704 or resid 71 \ 2 through 761 or (resid 762 and (name N or name CA or name C or name O or name C \ B )) or resid 763 through 841 or resid 896 through 903 or (resid 904 and (name N \ or name CA or name C or name O or name CB )) or resid 905 or (resid 906 through \ 908 and (name N or name CA or name C or name O or name CB )) or resid 909 throu \ gh 917 or (resid 918 through 919 and (name N or name CA or name C or name O or n \ ame CB )) or resid 920 through 953 or (resid 957 through 958 and (name N or name \ CA or name C or name O or name CB )) or resid 959 through 1123 or (resid 1124 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1125 or (resid \ 1126 and (name N or name CA or name C or name O or name CB )) or resid 1127)) selection = (chain 'B' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 621 or (resid 622 and (name N or name CA or name C \ or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA or nam \ e C or name O or name CB )) or resid 625 through 628 or (resid 629 and (name N o \ r name CA or name C or name O or name CB )) or resid 630 through 704 or resid 71 \ 2 through 761 or (resid 762 and (name N or name CA or name C or name O or name C \ B )) or resid 763 through 905 or (resid 906 through 908 and (name N or name CA o \ r name C or name O or name CB )) or resid 909 through 917 or (resid 918 through \ 919 and (name N or name CA or name C or name O or name CB )) or resid 920 throug \ h 953 or (resid 957 through 958 and (name N or name CA or name C or name O or na \ me CB )) or resid 959 through 1030 or resid 1032 through 1123 or (resid 1124 and \ (name N or name CA or name C or name O or name CB )) or resid 1125 or (resid 11 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 1127)) selection = (chain 'C' and (resid 585 through 621 or (resid 622 and (name N or name CA or na \ me C or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA o \ r name C or name O or name CB )) or resid 625 through 637 or (resid 638 and (nam \ e N or name CA or name C or name O or name CB )) or resid 639 through 702 or (re \ sid 703 and (name N or name CA or name C or name O or name CB )) or resid 704 or \ resid 712 through 761 or (resid 762 and (name N or name CA or name C or name O \ or name CB )) or resid 763 through 841 or resid 896 through 906 or (resid 907 th \ rough 908 and (name N or name CA or name C or name O or name CB )) or resid 909 \ through 917 or (resid 918 through 919 and (name N or name CA or name C or name O \ or name CB )) or resid 920 through 953 or (resid 957 through 958 and (name N or \ name CA or name C or name O or name CB )) or resid 959 through 1030 or resid 10 \ 32 through 1123 or (resid 1124 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1125 or (resid 1126 and (name N or name CA or name C or name O \ or name CB )) or resid 1127)) selection = (chain 'D' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 621 or (resid 622 and (name N or name CA or name C \ or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA or nam \ e C or name O or name CB )) or resid 625 through 628 or (resid 629 and (name N o \ r name CA or name C or name O or name CB )) or resid 630 through 637 or (resid 6 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 639 through \ 702 or (resid 703 and (name N or name CA or name C or name O or name CB )) or r \ esid 704 or resid 712 through 841 or resid 896 through 903 or (resid 904 and (na \ me N or name CA or name C or name O or name CB )) or resid 905 or (resid 906 thr \ ough 908 and (name N or name CA or name C or name O or name CB )) or resid 909 t \ hrough 917 or (resid 918 through 919 and (name N or name CA or name C or name O \ or name CB )) or resid 920 through 953 or (resid 957 through 958 and (name N or \ name CA or name C or name O or name CB )) or resid 959 through 1030 or resid 103 \ 2 through 1127)) selection = (chain 'E' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 621 or (resid 622 and (name N or name CA or name C \ or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA or nam \ e C or name O or name CB )) or resid 625 through 637 or (resid 638 and (name N o \ r name CA or name C or name O or name CB )) or resid 639 through 702 or (resid 7 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 704 or resi \ d 712 through 761 or (resid 762 and (name N or name CA or name C or name O or na \ me CB )) or resid 763 through 841 or resid 896 through 903 or (resid 904 and (na \ me N or name CA or name C or name O or name CB )) or resid 905 or (resid 906 thr \ ough 908 and (name N or name CA or name C or name O or name CB )) or resid 909 t \ hrough 917 or (resid 918 through 919 and (name N or name CA or name C or name O \ or name CB )) or resid 920 through 953 or (resid 957 through 958 and (name N or \ name CA or name C or name O or name CB )) or resid 959 through 1030 or resid 103 \ 2 through 1123 or (resid 1124 and (name N or name CA or name C or name O or name \ CB )) or resid 1125 or (resid 1126 and (name N or name CA or name C or name O o \ r name CB )) or resid 1127)) selection = (chain 'F' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 621 or (resid 622 and (name N or name CA or name C \ or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA or nam \ e C or name O or name CB )) or resid 625 through 628 or (resid 629 and (name N o \ r name CA or name C or name O or name CB )) or resid 630 through 637 or (resid 6 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 639 through \ 702 or (resid 703 and (name N or name CA or name C or name O or name CB )) or r \ esid 704 or resid 712 through 761 or (resid 762 and (name N or name CA or name C \ or name O or name CB )) or resid 763 through 903 or (resid 904 and (name N or n \ ame CA or name C or name O or name CB )) or resid 905 or (resid 906 through 908 \ and (name N or name CA or name C or name O or name CB )) or resid 909 through 95 \ 3 or (resid 957 through 958 and (name N or name CA or name C or name O or name C \ B )) or resid 959 through 1030 or resid 1032 through 1125 or (resid 1126 and (na \ me N or name CA or name C or name O or name CB )) or resid 1127)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.830 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 53.110 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.002 0.088 25377 Z= 0.156 Angle : 0.649 36.718 34331 Z= 0.376 Chirality : 0.045 0.946 3891 Planarity : 0.005 0.084 4343 Dihedral : 14.857 124.418 9657 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.02 % Favored : 94.85 % Rotamer: Outliers : 0.07 % Allowed : 0.19 % Favored : 99.74 % Cbeta Deviations : 0.03 % 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: -0.70 (0.15), residues: 3128 helix: 0.53 (0.15), residues: 1363 sheet: -0.45 (0.24), residues: 474 loop : -1.52 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 934 HIS 0.005 0.001 HIS A 957 PHE 0.015 0.001 PHE C1024 TYR 0.014 0.001 TYR D 812 ARG 0.008 0.000 ARG D 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 326 time to evaluate : 2.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5482 (m-10) cc_final: 0.4767 (m-10) REVERT: C 628 ILE cc_start: 0.7778 (mp) cc_final: 0.7568 (mp) REVERT: C 661 MET cc_start: 0.2022 (tmm) cc_final: 0.1113 (ttp) REVERT: C 810 MET cc_start: 0.6460 (ppp) cc_final: 0.5703 (ptm) REVERT: D 920 LEU cc_start: 0.4602 (mp) cc_final: 0.3209 (tt) REVERT: E 546 ILE cc_start: 0.8397 (mm) cc_final: 0.8060 (mm) REVERT: F 531 LYS cc_start: 0.5901 (mptt) cc_final: 0.5503 (mmtm) REVERT: F 904 LYS cc_start: 0.8516 (ptmm) cc_final: 0.8294 (ttpp) outliers start: 2 outliers final: 0 residues processed: 328 average time/residue: 0.3927 time to fit residues: 196.1128 Evaluate side-chains 271 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 283 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 798 HIS B1078 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN ** D 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 726 ASN E 693 ASN ** E 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 569 ASN ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25377 Z= 0.214 Angle : 0.588 9.766 34331 Z= 0.294 Chirality : 0.043 0.198 3891 Planarity : 0.005 0.062 4343 Dihedral : 8.069 114.351 3538 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.15 % Favored : 94.73 % Rotamer: Outliers : 0.37 % Allowed : 6.76 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.15), residues: 3128 helix: 0.79 (0.14), residues: 1373 sheet: -0.42 (0.24), residues: 462 loop : -1.59 (0.17), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 934 HIS 0.008 0.001 HIS A 798 PHE 0.021 0.002 PHE C 613 TYR 0.020 0.001 TYR B 978 ARG 0.005 0.000 ARG E1064 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 297 time to evaluate : 2.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5362 (m-10) cc_final: 0.4827 (m-10) REVERT: B 649 LEU cc_start: 0.6140 (tp) cc_final: 0.5676 (mt) REVERT: B 801 MET cc_start: 0.8458 (mmm) cc_final: 0.8250 (mmm) REVERT: C 626 LYS cc_start: 0.7445 (tmtt) cc_final: 0.7152 (tmtt) REVERT: C 628 ILE cc_start: 0.7834 (mp) cc_final: 0.7560 (mp) REVERT: C 810 MET cc_start: 0.6208 (ppp) cc_final: 0.5347 (ttt) REVERT: D 798 HIS cc_start: 0.5116 (m90) cc_final: 0.4806 (m170) REVERT: D 920 LEU cc_start: 0.5028 (mp) cc_final: 0.3419 (tt) REVERT: D 978 TYR cc_start: 0.5540 (m-80) cc_final: 0.5203 (m-80) REVERT: E 568 ARG cc_start: 0.8342 (ttp-110) cc_final: 0.7632 (ttp80) REVERT: F 904 LYS cc_start: 0.8634 (ptmm) cc_final: 0.8366 (tmmt) outliers start: 10 outliers final: 7 residues processed: 302 average time/residue: 0.4028 time to fit residues: 185.3569 Evaluate side-chains 269 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 262 time to evaluate : 2.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain F residue 569 ASN Chi-restraints excluded: chain F residue 572 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 0.0870 chunk 192 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 252 optimal weight: 0.0270 chunk 281 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 227 optimal weight: 3.9990 overall best weight: 2.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 GLN B1078 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 HIS ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 670 HIS ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 25377 Z= 0.300 Angle : 0.615 9.113 34331 Z= 0.306 Chirality : 0.044 0.228 3891 Planarity : 0.005 0.061 4343 Dihedral : 7.967 111.398 3538 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.53 % Favored : 94.37 % Rotamer: Outliers : 0.82 % Allowed : 9.43 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.15), residues: 3128 helix: 0.80 (0.14), residues: 1376 sheet: -0.42 (0.24), residues: 457 loop : -1.67 (0.17), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1119 HIS 0.006 0.001 HIS A 798 PHE 0.038 0.002 PHE C 960 TYR 0.024 0.001 TYR C 978 ARG 0.005 0.000 ARG E1064 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 277 time to evaluate : 2.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 674 TYR cc_start: 0.5721 (m-80) cc_final: 0.5477 (m-80) REVERT: A 960 PHE cc_start: 0.5603 (m-10) cc_final: 0.4918 (m-10) REVERT: A 983 MET cc_start: 0.8564 (tpt) cc_final: 0.8346 (tpt) REVERT: C 628 ILE cc_start: 0.7868 (mp) cc_final: 0.7611 (mp) REVERT: C 810 MET cc_start: 0.6233 (ppp) cc_final: 0.5561 (ttt) REVERT: D 603 MET cc_start: 0.8294 (ptp) cc_final: 0.8072 (mtm) REVERT: D 798 HIS cc_start: 0.5143 (m90) cc_final: 0.4604 (m170) REVERT: D 978 TYR cc_start: 0.5966 (m-80) cc_final: 0.5518 (m-80) REVERT: E 568 ARG cc_start: 0.8332 (ttp-110) cc_final: 0.7562 (ttp80) REVERT: F 904 LYS cc_start: 0.8663 (ptmm) cc_final: 0.8408 (tmmt) outliers start: 22 outliers final: 6 residues processed: 291 average time/residue: 0.4000 time to fit residues: 178.9357 Evaluate side-chains 262 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 256 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 922 GLU Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 135 optimal weight: 1.9990 chunk 190 optimal weight: 0.9980 chunk 284 optimal weight: 1.9990 chunk 301 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 269 optimal weight: 2.9990 chunk 81 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25377 Z= 0.201 Angle : 0.569 8.251 34331 Z= 0.283 Chirality : 0.042 0.208 3891 Planarity : 0.004 0.062 4343 Dihedral : 7.798 108.296 3538 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.43 % Favored : 94.47 % Rotamer: Outliers : 0.82 % Allowed : 11.43 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.15), residues: 3128 helix: 0.94 (0.14), residues: 1377 sheet: -0.46 (0.24), residues: 457 loop : -1.64 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 934 HIS 0.005 0.001 HIS A 798 PHE 0.035 0.001 PHE C 960 TYR 0.021 0.001 TYR C 978 ARG 0.005 0.000 ARG E 655 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 268 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 TYR cc_start: 0.5597 (m-80) cc_final: 0.5376 (m-80) REVERT: A 960 PHE cc_start: 0.5570 (m-10) cc_final: 0.5006 (m-10) REVERT: C 810 MET cc_start: 0.6009 (ppp) cc_final: 0.5521 (ttt) REVERT: D 978 TYR cc_start: 0.5992 (m-80) cc_final: 0.5532 (m-80) REVERT: E 568 ARG cc_start: 0.8265 (ttp-110) cc_final: 0.7557 (ttp80) REVERT: F 904 LYS cc_start: 0.8667 (ptmm) cc_final: 0.8426 (tmmt) outliers start: 22 outliers final: 8 residues processed: 283 average time/residue: 0.4010 time to fit residues: 173.6442 Evaluate side-chains 262 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 254 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 922 GLU Chi-restraints excluded: chain F residue 572 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 270 optimal weight: 0.4980 chunk 76 optimal weight: 6.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN F 544 GLN ** F 693 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 25377 Z= 0.355 Angle : 0.655 9.238 34331 Z= 0.326 Chirality : 0.045 0.187 3891 Planarity : 0.005 0.061 4343 Dihedral : 7.926 106.199 3538 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.01 % Favored : 93.89 % Rotamer: Outliers : 1.15 % Allowed : 12.21 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.72 (0.15), residues: 3128 helix: 0.78 (0.14), residues: 1384 sheet: -0.71 (0.24), residues: 465 loop : -1.79 (0.17), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C1119 HIS 0.005 0.001 HIS E1003 PHE 0.041 0.002 PHE C 960 TYR 0.026 0.002 TYR C 978 ARG 0.005 0.000 ARG E1064 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 279 time to evaluate : 3.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5775 (m-10) cc_final: 0.5189 (m-10) REVERT: A 983 MET cc_start: 0.8495 (tpt) cc_final: 0.8185 (tpt) REVERT: B 591 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7282 (ttp80) REVERT: C 810 MET cc_start: 0.5937 (ppp) cc_final: 0.5533 (ttt) REVERT: C 903 GLN cc_start: 0.6750 (tm-30) cc_final: 0.6540 (tm-30) REVERT: D 816 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.6534 (pp20) REVERT: D 978 TYR cc_start: 0.6200 (m-80) cc_final: 0.5628 (m-80) REVERT: E 568 ARG cc_start: 0.8250 (ttp-110) cc_final: 0.7520 (ttp80) REVERT: F 904 LYS cc_start: 0.8633 (ptmm) cc_final: 0.8429 (tmmt) REVERT: F 1043 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8023 (pt) outliers start: 31 outliers final: 13 residues processed: 299 average time/residue: 0.4225 time to fit residues: 191.3062 Evaluate side-chains 270 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 254 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain D residue 816 GLU Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain E residue 935 THR Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 1043 LEU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 4.9990 chunk 271 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 301 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN F 693 ASN ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25377 Z= 0.201 Angle : 0.590 11.214 34331 Z= 0.294 Chirality : 0.042 0.191 3891 Planarity : 0.004 0.062 4343 Dihedral : 7.736 103.636 3538 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.50 % Favored : 94.41 % Rotamer: Outliers : 1.11 % Allowed : 13.36 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.53 (0.15), residues: 3128 helix: 1.00 (0.14), residues: 1372 sheet: -0.73 (0.23), residues: 468 loop : -1.69 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 934 HIS 0.006 0.001 HIS A 798 PHE 0.020 0.001 PHE C 960 TYR 0.021 0.001 TYR C 978 ARG 0.007 0.000 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 258 time to evaluate : 2.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5491 (m-10) cc_final: 0.5083 (m-10) REVERT: A 983 MET cc_start: 0.8409 (tpt) cc_final: 0.7962 (tpt) REVERT: B 591 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7278 (ttp80) REVERT: C 978 TYR cc_start: 0.6445 (m-10) cc_final: 0.5790 (m-80) REVERT: D 978 TYR cc_start: 0.6069 (m-80) cc_final: 0.5515 (m-80) REVERT: E 568 ARG cc_start: 0.8226 (ttp-110) cc_final: 0.7535 (ttp80) REVERT: F 904 LYS cc_start: 0.8644 (ptmm) cc_final: 0.8420 (ttpp) REVERT: F 1043 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.7954 (pt) outliers start: 30 outliers final: 12 residues processed: 281 average time/residue: 0.4027 time to fit residues: 173.1432 Evaluate side-chains 259 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 245 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 582 HIS Chi-restraints excluded: chain D residue 747 CYS Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 1043 LEU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 0.0470 chunk 34 optimal weight: 0.1980 chunk 171 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 300 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.8484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 684 GLN F 582 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25377 Z= 0.270 Angle : 0.611 8.860 34331 Z= 0.304 Chirality : 0.043 0.180 3891 Planarity : 0.005 0.062 4343 Dihedral : 7.714 101.405 3538 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.95 % Favored : 93.96 % Rotamer: Outliers : 1.04 % Allowed : 13.55 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.61 (0.15), residues: 3128 helix: 0.94 (0.14), residues: 1379 sheet: -0.75 (0.23), residues: 473 loop : -1.78 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 934 HIS 0.005 0.001 HIS F 798 PHE 0.022 0.002 PHE E 960 TYR 0.023 0.001 TYR C 978 ARG 0.007 0.000 ARG E 655 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 260 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 937 MET cc_start: 0.8221 (mmt) cc_final: 0.7679 (mmp) REVERT: A 960 PHE cc_start: 0.5600 (m-10) cc_final: 0.5182 (m-10) REVERT: A 983 MET cc_start: 0.8456 (tpt) cc_final: 0.8001 (tpt) REVERT: B 591 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.7290 (ttp80) REVERT: C 661 MET cc_start: 0.2731 (tmm) cc_final: 0.2135 (ttp) REVERT: D 816 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6568 (pp20) REVERT: D 978 TYR cc_start: 0.6168 (m-80) cc_final: 0.5492 (m-80) REVERT: F 1043 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8018 (pt) outliers start: 28 outliers final: 18 residues processed: 280 average time/residue: 0.3870 time to fit residues: 166.0369 Evaluate side-chains 276 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 255 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 697 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 816 GLU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 777 VAL Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 917 THR Chi-restraints excluded: chain F residue 1043 LEU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 2.9990 chunk 120 optimal weight: 8.9990 chunk 179 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 191 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 236 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1078 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 HIS C 821 ASN F 569 ASN ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25377 Z= 0.170 Angle : 0.574 9.126 34331 Z= 0.285 Chirality : 0.042 0.191 3891 Planarity : 0.004 0.061 4343 Dihedral : 7.511 98.371 3538 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.05 % Favored : 94.85 % Rotamer: Outliers : 0.93 % Allowed : 13.88 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 3128 helix: 1.13 (0.14), residues: 1374 sheet: -0.67 (0.23), residues: 483 loop : -1.67 (0.17), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 934 HIS 0.007 0.001 HIS C 953 PHE 0.017 0.001 PHE D 653 TYR 0.012 0.001 TYR C 978 ARG 0.005 0.000 ARG A 672 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 263 time to evaluate : 3.002 Fit side-chains revert: symmetry clash REVERT: A 937 MET cc_start: 0.8188 (mmt) cc_final: 0.7526 (mmp) REVERT: A 960 PHE cc_start: 0.5344 (m-10) cc_final: 0.5048 (m-10) REVERT: A 983 MET cc_start: 0.8355 (tpt) cc_final: 0.7895 (tpt) REVERT: C 661 MET cc_start: 0.2662 (tmm) cc_final: 0.1831 (ttp) REVERT: C 978 TYR cc_start: 0.6256 (m-10) cc_final: 0.5947 (m-80) REVERT: D 978 TYR cc_start: 0.6080 (m-80) cc_final: 0.5502 (m-80) REVERT: E 703 LYS cc_start: 0.7950 (mmtt) cc_final: 0.7369 (mttt) REVERT: E 1039 MET cc_start: 0.9168 (ptm) cc_final: 0.8929 (ptm) REVERT: F 1043 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.7916 (pt) outliers start: 25 outliers final: 17 residues processed: 278 average time/residue: 0.3908 time to fit residues: 167.7742 Evaluate side-chains 266 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 248 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain E residue 985 LEU Chi-restraints excluded: chain F residue 569 ASN Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 1043 LEU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 3.9990 chunk 288 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 280 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 220 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 chunk 253 optimal weight: 0.7980 chunk 265 optimal weight: 5.9990 chunk 279 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS B 586 GLN ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 HIS ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 569 ASN ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25377 Z= 0.202 Angle : 0.589 10.275 34331 Z= 0.292 Chirality : 0.042 0.259 3891 Planarity : 0.004 0.059 4343 Dihedral : 7.487 97.076 3538 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 0.97 % Allowed : 13.99 % Favored : 85.04 % 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: -0.40 (0.15), residues: 3128 helix: 1.15 (0.14), residues: 1375 sheet: -0.68 (0.23), residues: 487 loop : -1.68 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 934 HIS 0.005 0.001 HIS F 798 PHE 0.019 0.001 PHE D 653 TYR 0.017 0.001 TYR C 978 ARG 0.007 0.000 ARG B 591 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 249 time to evaluate : 2.823 Fit side-chains revert: symmetry clash REVERT: A 937 MET cc_start: 0.8199 (mmt) cc_final: 0.7532 (mmp) REVERT: A 960 PHE cc_start: 0.5458 (m-10) cc_final: 0.5084 (m-10) REVERT: A 983 MET cc_start: 0.8380 (tpt) cc_final: 0.7905 (tpt) REVERT: C 661 MET cc_start: 0.2438 (tmm) cc_final: 0.1999 (ttp) REVERT: C 978 TYR cc_start: 0.6474 (m-10) cc_final: 0.5766 (m-80) REVERT: D 816 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6530 (pp20) REVERT: D 978 TYR cc_start: 0.6162 (m-80) cc_final: 0.5463 (m-80) REVERT: E 670 HIS cc_start: 0.8443 (OUTLIER) cc_final: 0.7326 (m90) REVERT: E 703 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7380 (mttt) REVERT: F 763 MET cc_start: 0.8117 (mtm) cc_final: 0.7874 (mtm) REVERT: F 1043 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.7917 (pt) outliers start: 26 outliers final: 18 residues processed: 268 average time/residue: 0.4142 time to fit residues: 171.6758 Evaluate side-chains 267 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 246 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 816 GLU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain E residue 670 HIS Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain E residue 985 LEU Chi-restraints excluded: chain F residue 569 ASN Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 917 THR Chi-restraints excluded: chain F residue 1043 LEU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 140 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 310 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 247 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 569 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25377 Z= 0.206 Angle : 0.595 10.188 34331 Z= 0.295 Chirality : 0.043 0.256 3891 Planarity : 0.004 0.059 4343 Dihedral : 7.463 95.151 3538 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.75 % Favored : 94.18 % Rotamer: Outliers : 0.85 % Allowed : 14.14 % Favored : 85.00 % 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: -0.38 (0.15), residues: 3128 helix: 1.16 (0.14), residues: 1369 sheet: -0.65 (0.23), residues: 478 loop : -1.66 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 934 HIS 0.008 0.001 HIS C 798 PHE 0.019 0.001 PHE D 653 TYR 0.018 0.001 TYR C 978 ARG 0.007 0.000 ARG B 591 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6256 Ramachandran restraints generated. 3128 Oldfield, 0 Emsley, 3128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 247 time to evaluate : 2.976 Fit side-chains revert: symmetry clash REVERT: A 937 MET cc_start: 0.8206 (mmt) cc_final: 0.7538 (mmp) REVERT: A 960 PHE cc_start: 0.5509 (m-10) cc_final: 0.5128 (m-10) REVERT: A 983 MET cc_start: 0.8383 (tpt) cc_final: 0.7902 (tpt) REVERT: B 1122 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7784 (pm20) REVERT: C 661 MET cc_start: 0.2422 (tmm) cc_final: 0.1983 (ttp) REVERT: C 978 TYR cc_start: 0.6532 (m-10) cc_final: 0.5822 (m-80) REVERT: D 816 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.6532 (pp20) REVERT: D 950 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7158 (pt0) REVERT: D 978 TYR cc_start: 0.6169 (m-80) cc_final: 0.5486 (m-80) REVERT: E 703 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7381 (mttt) REVERT: F 763 MET cc_start: 0.8090 (mtm) cc_final: 0.7853 (mtm) REVERT: F 1043 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.7917 (pt) outliers start: 23 outliers final: 18 residues processed: 262 average time/residue: 0.3985 time to fit residues: 160.0474 Evaluate side-chains 266 residues out of total 2721 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 614 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 1122 GLU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain D residue 816 GLU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain E residue 985 LEU Chi-restraints excluded: chain F residue 569 ASN Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 810 MET Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 1043 LEU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 247 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS ** B 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.159683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.122032 restraints weight = 34509.671| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.12 r_work: 0.3053 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 25377 Z= 0.300 Angle : 0.643 10.317 34331 Z= 0.319 Chirality : 0.044 0.251 3891 Planarity : 0.005 0.099 4343 Dihedral : 7.613 92.567 3538 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.20 % Favored : 93.73 % Rotamer: Outliers : 0.97 % Allowed : 13.99 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3128 helix: 0.98 (0.14), residues: 1382 sheet: -0.64 (0.24), residues: 471 loop : -1.77 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 573 HIS 0.007 0.001 HIS C 798 PHE 0.025 0.002 PHE C 960 TYR 0.026 0.002 TYR C 978 ARG 0.007 0.000 ARG B 591 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4860.60 seconds wall clock time: 88 minutes 21.69 seconds (5301.69 seconds total)