Starting phenix.real_space_refine on Sat Jun 21 17:10:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxo_25502/06_2025/7sxo_25502.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxo_25502/06_2025/7sxo_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/cci-nas-00/data/ceres_data/7sxo_25502/06_2025/7sxo_25502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxo_25502/06_2025/7sxo_25502.map" model { file = "/net/cci-nas-00/data/ceres_data/7sxo_25502/06_2025/7sxo_25502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxo_25502/06_2025/7sxo_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-5710/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: 15.80, per 1000 atoms: 0.63 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: 6.13 Conformation dependent library (CDL) restraints added in 3.5 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: 3.03 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: 8.24 Time building geometry restraints manager: 7.21 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: 1.270 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: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 56.470 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.720 ------------------------------------------------------------------------------- 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 25384 Z= 0.125 Angle : 0.650 36.718 34339 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 Details of bonding type rmsd hydrogen bonds : bond 0.16020 ( 1016) hydrogen bonds : angle 6.59544 ( 2970) SS BOND : bond 0.00384 ( 4) SS BOND : angle 2.11977 ( 8) covalent geometry : bond 0.00243 (25377) covalent geometry : angle 0.64909 (34331) Misc. bond : bond 0.00259 ( 3) *********************** 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 to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 3.089 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: 0.3905 time to fit residues: 196.5729 Evaluate side-chains 271 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 3.184 ------------------------------------------------------------------------------- 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.164531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.127193 restraints weight = 34547.736| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.11 r_work: 0.3134 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 25384 Z= 0.139 Angle : 0.588 9.768 34339 Z= 0.294 Chirality : 0.043 0.198 3891 Planarity : 0.005 0.062 4343 Dihedral : 8.069 114.341 3538 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.83 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 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 1016) hydrogen bonds : angle 4.88581 ( 2970) SS BOND : bond 0.00224 ( 4) SS BOND : angle 1.54679 ( 8) covalent geometry : bond 0.00326 (25377) covalent geometry : angle 0.58790 (34331) Misc. bond : bond 0.00221 ( 3) *********************** 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 to be fit. rotamer outliers: 10 poor density : 297 time to evaluate : 2.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5871 (m-10) cc_final: 0.5250 (m-10) REVERT: B 649 LEU cc_start: 0.6791 (tp) cc_final: 0.6077 (mt) REVERT: B 801 MET cc_start: 0.8577 (mmm) cc_final: 0.8349 (mmm) REVERT: C 626 LYS cc_start: 0.7330 (tmtt) cc_final: 0.6943 (tmtt) REVERT: C 763 MET cc_start: 0.6832 (OUTLIER) cc_final: 0.5940 (tpt) REVERT: C 810 MET cc_start: 0.6895 (ppp) cc_final: 0.6025 (ttt) REVERT: C 827 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8237 (mt-10) REVERT: D 725 GLN cc_start: 0.7709 (mt0) cc_final: 0.7377 (mm-40) REVERT: D 798 HIS cc_start: 0.5919 (m90) cc_final: 0.5305 (m170) REVERT: D 920 LEU cc_start: 0.5167 (mp) cc_final: 0.3421 (tt) REVERT: D 978 TYR cc_start: 0.6138 (m-80) cc_final: 0.5659 (m-80) REVERT: E 546 ILE cc_start: 0.7844 (mm) cc_final: 0.7599 (mm) REVERT: E 568 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.7611 (ttp80) REVERT: F 904 LYS cc_start: 0.8845 (ptmm) cc_final: 0.8569 (tmmt) outliers start: 10 outliers final: 7 residues processed: 302 average time/residue: 0.4108 time to fit residues: 190.3631 Evaluate side-chains 272 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 264 time to evaluate : 3.108 ------------------------------------------------------------------------------- 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 763 MET 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 32 optimal weight: 0.0970 chunk 195 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 242 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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** B1078 ASN ** D 693 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.165204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127274 restraints weight = 34247.153| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.07 r_work: 0.3157 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25384 Z= 0.112 Angle : 0.553 9.377 34339 Z= 0.275 Chirality : 0.041 0.221 3891 Planarity : 0.004 0.061 4343 Dihedral : 7.813 110.378 3538 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.76 % Rotamer: Outliers : 0.67 % Allowed : 8.95 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 3128 helix: 0.99 (0.14), residues: 1369 sheet: -0.47 (0.24), residues: 472 loop : -1.58 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 934 HIS 0.006 0.001 HIS A 798 PHE 0.030 0.001 PHE C 960 TYR 0.016 0.001 TYR C 978 ARG 0.005 0.000 ARG E 831 Details of bonding type rmsd hydrogen bonds : bond 0.03253 ( 1016) hydrogen bonds : angle 4.58794 ( 2970) SS BOND : bond 0.00164 ( 4) SS BOND : angle 1.37807 ( 8) covalent geometry : bond 0.00257 (25377) covalent geometry : angle 0.55311 (34331) Misc. bond : bond 0.00203 ( 3) *********************** 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 293 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 275 time to evaluate : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 GLU cc_start: 0.8526 (pp20) cc_final: 0.8275 (pp20) REVERT: A 960 PHE cc_start: 0.5895 (m-10) cc_final: 0.5307 (m-10) REVERT: C 763 MET cc_start: 0.6781 (ttp) cc_final: 0.6127 (tpt) REVERT: C 934 TRP cc_start: 0.8786 (t60) cc_final: 0.8585 (t60) REVERT: D 725 GLN cc_start: 0.7795 (mt0) cc_final: 0.7386 (mm-40) REVERT: D 798 HIS cc_start: 0.5856 (m90) cc_final: 0.5127 (m170) REVERT: D 920 LEU cc_start: 0.5037 (mp) cc_final: 0.3289 (tt) REVERT: D 978 TYR cc_start: 0.6238 (m-80) cc_final: 0.5645 (m-80) REVERT: E 546 ILE cc_start: 0.7826 (mm) cc_final: 0.7542 (mm) REVERT: E 568 ARG cc_start: 0.8162 (ttp-110) cc_final: 0.7514 (ttp80) REVERT: E 937 MET cc_start: 0.8238 (tmm) cc_final: 0.7998 (tmm) REVERT: F 904 LYS cc_start: 0.8845 (ptmm) cc_final: 0.8588 (tmmt) outliers start: 18 outliers final: 6 residues processed: 288 average time/residue: 0.4226 time to fit residues: 187.5772 Evaluate side-chains 267 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 261 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 LEU 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 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 213 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 283 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 214 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 177 optimal weight: 0.9980 chunk 293 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 836 GLN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 HIS C 821 ASN D 693 ASN E 670 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.163510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.126045 restraints weight = 34425.561| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 3.31 r_work: 0.3147 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25384 Z= 0.124 Angle : 0.559 9.311 34339 Z= 0.276 Chirality : 0.042 0.192 3891 Planarity : 0.004 0.059 4343 Dihedral : 7.637 107.006 3538 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 1.04 % Allowed : 10.02 % Favored : 88.94 % 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: -0.35 (0.15), residues: 3128 helix: 1.10 (0.14), residues: 1366 sheet: -0.37 (0.24), residues: 459 loop : -1.64 (0.17), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1119 HIS 0.003 0.001 HIS F 798 PHE 0.031 0.001 PHE C 960 TYR 0.020 0.001 TYR C 978 ARG 0.004 0.000 ARG E1056 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 1016) hydrogen bonds : angle 4.41305 ( 2970) SS BOND : bond 0.00171 ( 4) SS BOND : angle 1.54988 ( 8) covalent geometry : bond 0.00292 (25377) covalent geometry : angle 0.55822 (34331) Misc. bond : bond 0.00202 ( 3) *********************** 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 303 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 275 time to evaluate : 3.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 TRP cc_start: 0.8335 (m100) cc_final: 0.8131 (m100) REVERT: A 674 TYR cc_start: 0.5424 (m-80) cc_final: 0.5001 (m-80) REVERT: A 960 PHE cc_start: 0.5873 (m-10) cc_final: 0.5234 (m-10) REVERT: A 983 MET cc_start: 0.9039 (tpt) cc_final: 0.8814 (tpt) REVERT: C 661 MET cc_start: 0.2869 (tmm) cc_final: 0.2593 (ttp) REVERT: C 763 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.5970 (tpt) REVERT: C 810 MET cc_start: 0.6964 (ppp) cc_final: 0.6451 (ttt) REVERT: C 827 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8264 (mt-10) REVERT: D 725 GLN cc_start: 0.7811 (mt0) cc_final: 0.7286 (mm-40) REVERT: D 978 TYR cc_start: 0.6316 (m-80) cc_final: 0.5703 (m-80) REVERT: E 546 ILE cc_start: 0.7849 (mm) cc_final: 0.7567 (mm) REVERT: E 568 ARG cc_start: 0.8145 (ttp-110) cc_final: 0.7492 (ttp80) REVERT: E 937 MET cc_start: 0.8219 (tmm) cc_final: 0.7939 (tmm) REVERT: F 904 LYS cc_start: 0.8848 (ptmm) cc_final: 0.8634 (tmmt) outliers start: 28 outliers final: 14 residues processed: 292 average time/residue: 0.4083 time to fit residues: 183.2641 Evaluate side-chains 274 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 259 time to evaluate : 2.761 ------------------------------------------------------------------------------- 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 C residue 763 MET Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain D residue 922 GLU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain F residue 572 ASP Chi-restraints excluded: chain F residue 603 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 70 optimal weight: 7.9990 chunk 121 optimal weight: 0.3980 chunk 41 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 122 optimal weight: 0.0670 chunk 240 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.165266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127360 restraints weight = 34647.740| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 3.37 r_work: 0.3169 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 25384 Z= 0.102 Angle : 0.540 9.251 34339 Z= 0.268 Chirality : 0.041 0.177 3891 Planarity : 0.004 0.060 4343 Dihedral : 7.496 104.702 3538 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 0.89 % Allowed : 11.17 % Favored : 87.94 % 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: -0.23 (0.16), residues: 3128 helix: 1.23 (0.15), residues: 1365 sheet: -0.45 (0.24), residues: 472 loop : -1.56 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 934 HIS 0.003 0.000 HIS F 798 PHE 0.025 0.001 PHE C 960 TYR 0.018 0.001 TYR C 978 ARG 0.004 0.000 ARG E1056 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 1016) hydrogen bonds : angle 4.30672 ( 2970) SS BOND : bond 0.00166 ( 4) SS BOND : angle 1.81307 ( 8) covalent geometry : bond 0.00230 (25377) covalent geometry : angle 0.53923 (34331) Misc. bond : bond 0.00188 ( 3) *********************** 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 293 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 269 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 674 TYR cc_start: 0.5344 (m-80) cc_final: 0.4905 (m-80) REVERT: A 960 PHE cc_start: 0.5778 (m-10) cc_final: 0.5305 (m-10) REVERT: A 983 MET cc_start: 0.9015 (tpt) cc_final: 0.8763 (tpt) REVERT: B 591 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7478 (ttp80) REVERT: C 661 MET cc_start: 0.3051 (tmm) cc_final: 0.2757 (ttp) REVERT: C 763 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.5946 (tpt) REVERT: C 827 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8285 (mt-10) REVERT: C 978 TYR cc_start: 0.6562 (m-80) cc_final: 0.5771 (m-80) REVERT: D 725 GLN cc_start: 0.7757 (mt0) cc_final: 0.7208 (mm-40) REVERT: D 978 TYR cc_start: 0.6207 (m-80) cc_final: 0.5550 (m-80) REVERT: E 546 ILE cc_start: 0.7876 (mm) cc_final: 0.7592 (mm) REVERT: E 568 ARG cc_start: 0.8156 (ttp-110) cc_final: 0.7520 (ttp80) REVERT: E 718 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8318 (mp) REVERT: E 937 MET cc_start: 0.8265 (tmm) cc_final: 0.7970 (tmm) REVERT: F 904 LYS cc_start: 0.8853 (ptmm) cc_final: 0.8648 (tmmt) outliers start: 24 outliers final: 10 residues processed: 282 average time/residue: 0.4029 time to fit residues: 174.3701 Evaluate side-chains 266 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 253 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain D residue 922 GLU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain E residue 957 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 114 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 19 optimal weight: 7.9990 chunk 307 optimal weight: 0.0070 chunk 255 optimal weight: 0.5980 chunk 116 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 166 optimal weight: 7.9990 chunk 275 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1078 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 HIS C 821 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.165316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.127756 restraints weight = 34511.705| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.34 r_work: 0.3177 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25384 Z= 0.111 Angle : 0.555 12.844 34339 Z= 0.274 Chirality : 0.041 0.168 3891 Planarity : 0.004 0.058 4343 Dihedral : 7.425 102.809 3538 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.76 % Rotamer: Outliers : 1.04 % Allowed : 11.40 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.15), residues: 3128 helix: 1.24 (0.15), residues: 1371 sheet: -0.48 (0.24), residues: 472 loop : -1.57 (0.17), residues: 1285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 934 HIS 0.003 0.001 HIS F 798 PHE 0.020 0.001 PHE C 960 TYR 0.015 0.001 TYR C 978 ARG 0.004 0.000 ARG A 681 Details of bonding type rmsd hydrogen bonds : bond 0.02947 ( 1016) hydrogen bonds : angle 4.28749 ( 2970) SS BOND : bond 0.01099 ( 4) SS BOND : angle 3.33775 ( 8) covalent geometry : bond 0.00256 (25377) covalent geometry : angle 0.55253 (34331) Misc. bond : bond 0.00184 ( 3) *********************** 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 293 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 2.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 TYR cc_start: 0.5382 (m-80) cc_final: 0.5030 (m-80) REVERT: A 798 HIS cc_start: 0.3947 (m90) cc_final: 0.3496 (m-70) REVERT: A 960 PHE cc_start: 0.5805 (m-10) cc_final: 0.5273 (m-10) REVERT: A 983 MET cc_start: 0.9017 (tpt) cc_final: 0.8760 (tpt) REVERT: B 591 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7454 (ttp80) REVERT: C 810 MET cc_start: 0.7011 (ppp) cc_final: 0.6412 (ttt) REVERT: C 827 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8279 (mt-10) REVERT: D 725 GLN cc_start: 0.7759 (mt0) cc_final: 0.7186 (mm-40) REVERT: D 978 TYR cc_start: 0.6214 (m-80) cc_final: 0.5541 (m-80) REVERT: E 546 ILE cc_start: 0.7931 (mm) cc_final: 0.7670 (mm) REVERT: E 937 MET cc_start: 0.8257 (tmm) cc_final: 0.7953 (tmm) outliers start: 28 outliers final: 18 residues processed: 280 average time/residue: 0.3915 time to fit residues: 169.3206 Evaluate side-chains 274 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 255 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 920 LEU 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 C residue 1039 MET Chi-restraints excluded: chain D residue 747 CYS Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 922 GLU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain F residue 572 ASP 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 1110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 106 optimal weight: 8.9990 chunk 221 optimal weight: 9.9990 chunk 116 optimal weight: 0.4980 chunk 309 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 227 optimal weight: 0.0870 chunk 243 optimal weight: 2.9990 chunk 230 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 903 GLN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.162648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.124939 restraints weight = 34572.034| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.18 r_work: 0.3097 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25384 Z= 0.158 Angle : 0.591 10.826 34339 Z= 0.293 Chirality : 0.043 0.244 3891 Planarity : 0.004 0.058 4343 Dihedral : 7.485 100.894 3538 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.50 % Favored : 94.41 % Rotamer: Outliers : 0.93 % Allowed : 11.92 % Favored : 87.16 % 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: -0.32 (0.15), residues: 3128 helix: 1.13 (0.14), residues: 1376 sheet: -0.50 (0.24), residues: 468 loop : -1.59 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 934 HIS 0.009 0.001 HIS C 798 PHE 0.024 0.002 PHE C 960 TYR 0.024 0.001 TYR C 978 ARG 0.009 0.000 ARG A 672 Details of bonding type rmsd hydrogen bonds : bond 0.03305 ( 1016) hydrogen bonds : angle 4.36413 ( 2970) SS BOND : bond 0.00305 ( 4) SS BOND : angle 2.56503 ( 8) covalent geometry : bond 0.00380 (25377) covalent geometry : angle 0.58949 (34331) Misc. bond : bond 0.00207 ( 3) *********************** 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 to be fit. rotamer outliers: 25 poor density : 263 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5877 (m-10) cc_final: 0.5309 (m-10) REVERT: A 983 MET cc_start: 0.9072 (tpt) cc_final: 0.8860 (tpt) REVERT: B 591 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7490 (ttp80) REVERT: C 978 TYR cc_start: 0.6799 (m-80) cc_final: 0.5898 (m-80) REVERT: D 816 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6211 (pp20) REVERT: D 978 TYR cc_start: 0.6474 (m-80) cc_final: 0.5776 (m-80) REVERT: E 546 ILE cc_start: 0.7907 (mm) cc_final: 0.7640 (mm) REVERT: E 619 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8345 (mp) REVERT: E 937 MET cc_start: 0.8180 (tmm) cc_final: 0.7887 (tmm) REVERT: F 1043 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8156 (pt) outliers start: 25 outliers final: 13 residues processed: 280 average time/residue: 0.3844 time to fit residues: 165.8520 Evaluate side-chains 268 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 251 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain B residue 591 ARG 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 920 LEU Chi-restraints excluded: chain D residue 922 GLU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain F residue 572 ASP Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 736 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 122 optimal weight: 0.6980 chunk 234 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 117 optimal weight: 0.0000 chunk 135 optimal weight: 2.9990 chunk 242 optimal weight: 0.6980 chunk 258 optimal weight: 5.9990 chunk 283 optimal weight: 0.4980 chunk 127 optimal weight: 10.0000 chunk 58 optimal weight: 0.0000 overall best weight: 0.3788 ------------------------------------------------------------------------------- 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** B 726 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 693 ASN ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.165991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.128590 restraints weight = 34404.806| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 3.22 r_work: 0.3196 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25384 Z= 0.100 Angle : 0.554 9.917 34339 Z= 0.274 Chirality : 0.041 0.238 3891 Planarity : 0.004 0.058 4343 Dihedral : 7.304 98.015 3538 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.89 % Favored : 95.01 % Rotamer: Outliers : 0.78 % Allowed : 12.44 % Favored : 86.79 % 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: -0.15 (0.16), residues: 3128 helix: 1.32 (0.15), residues: 1369 sheet: -0.41 (0.24), residues: 461 loop : -1.54 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 934 HIS 0.007 0.001 HIS C 798 PHE 0.017 0.001 PHE D 653 TYR 0.013 0.001 TYR A 587 ARG 0.006 0.000 ARG A 672 Details of bonding type rmsd hydrogen bonds : bond 0.02754 ( 1016) hydrogen bonds : angle 4.22974 ( 2970) SS BOND : bond 0.00305 ( 4) SS BOND : angle 1.93552 ( 8) covalent geometry : bond 0.00225 (25377) covalent geometry : angle 0.55286 (34331) Misc. bond : bond 0.00179 ( 3) *********************** 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 292 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 271 time to evaluate : 2.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 937 MET cc_start: 0.8105 (mmp) cc_final: 0.7866 (mmp) REVERT: A 960 PHE cc_start: 0.5695 (m-10) cc_final: 0.5231 (m-10) REVERT: A 983 MET cc_start: 0.9048 (tpt) cc_final: 0.8811 (tpt) REVERT: C 763 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.5856 (tpt) REVERT: C 810 MET cc_start: 0.7033 (ppp) cc_final: 0.6562 (ttp) REVERT: C 978 TYR cc_start: 0.6555 (m-80) cc_final: 0.5705 (m-80) REVERT: D 950 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7256 (pt0) REVERT: D 978 TYR cc_start: 0.6182 (m-80) cc_final: 0.5524 (m-80) REVERT: E 546 ILE cc_start: 0.7964 (mm) cc_final: 0.7694 (mm) REVERT: F 1043 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8121 (pt) outliers start: 21 outliers final: 14 residues processed: 285 average time/residue: 0.3993 time to fit residues: 176.3283 Evaluate side-chains 273 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 257 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain F residue 572 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 102 optimal weight: 0.0070 chunk 16 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 233 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 197 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 684 GLN E 693 ASN F 582 HIS ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.164913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.127232 restraints weight = 34435.187| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.26 r_work: 0.3163 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25384 Z= 0.114 Angle : 0.570 10.371 34339 Z= 0.281 Chirality : 0.041 0.231 3891 Planarity : 0.004 0.084 4343 Dihedral : 7.259 96.195 3538 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 0.67 % Allowed : 12.88 % Favored : 86.45 % 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: -0.13 (0.16), residues: 3128 helix: 1.31 (0.15), residues: 1370 sheet: -0.43 (0.24), residues: 470 loop : -1.50 (0.17), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 934 HIS 0.009 0.001 HIS C 798 PHE 0.018 0.001 PHE D 653 TYR 0.016 0.001 TYR C 978 ARG 0.008 0.000 ARG E 655 Details of bonding type rmsd hydrogen bonds : bond 0.02896 ( 1016) hydrogen bonds : angle 4.21910 ( 2970) SS BOND : bond 0.00282 ( 4) SS BOND : angle 1.92083 ( 8) covalent geometry : bond 0.00268 (25377) covalent geometry : angle 0.56898 (34331) Misc. bond : bond 0.00177 ( 3) *********************** 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 282 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 264 time to evaluate : 2.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5609 (m-10) cc_final: 0.5118 (m-10) REVERT: A 983 MET cc_start: 0.9076 (tpt) cc_final: 0.8841 (tpt) REVERT: C 661 MET cc_start: 0.3432 (tmm) cc_final: 0.1995 (ttp) REVERT: C 810 MET cc_start: 0.7046 (ppp) cc_final: 0.6493 (ttp) REVERT: D 950 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7277 (pt0) REVERT: D 978 TYR cc_start: 0.6293 (m-80) cc_final: 0.5587 (m-80) REVERT: E 546 ILE cc_start: 0.7938 (mm) cc_final: 0.7685 (mm) REVERT: F 1043 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8089 (pt) outliers start: 18 outliers final: 12 residues processed: 277 average time/residue: 0.3831 time to fit residues: 164.5194 Evaluate side-chains 272 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 259 time to evaluate : 2.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 957 HIS 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 88 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 218 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 189 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 222 optimal weight: 0.6980 chunk 269 optimal weight: 0.7980 chunk 276 optimal weight: 5.9990 chunk 268 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1078 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 582 HIS ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.164730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.127320 restraints weight = 34361.261| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.99 r_work: 0.3149 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25384 Z= 0.117 Angle : 0.573 10.932 34339 Z= 0.283 Chirality : 0.042 0.235 3891 Planarity : 0.004 0.057 4343 Dihedral : 7.240 93.964 3538 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.27 % Favored : 94.63 % Rotamer: Outliers : 0.71 % Allowed : 12.99 % Favored : 86.30 % 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: -0.12 (0.16), residues: 3128 helix: 1.33 (0.15), residues: 1370 sheet: -0.38 (0.24), residues: 462 loop : -1.52 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 934 HIS 0.008 0.001 HIS C 798 PHE 0.021 0.001 PHE C 960 TYR 0.017 0.001 TYR C 978 ARG 0.005 0.000 ARG A 681 Details of bonding type rmsd hydrogen bonds : bond 0.02912 ( 1016) hydrogen bonds : angle 4.22085 ( 2970) SS BOND : bond 0.00278 ( 4) SS BOND : angle 1.91836 ( 8) covalent geometry : bond 0.00276 (25377) covalent geometry : angle 0.57255 (34331) Misc. bond : bond 0.00180 ( 3) ********************** 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 279 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 260 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5679 (m-10) cc_final: 0.5197 (m-10) REVERT: A 983 MET cc_start: 0.9006 (tpt) cc_final: 0.8747 (tpt) REVERT: B 810 MET cc_start: 0.7348 (tmm) cc_final: 0.6976 (ptt) REVERT: C 810 MET cc_start: 0.7076 (ppp) cc_final: 0.6661 (ttp) REVERT: C 978 TYR cc_start: 0.6609 (m-80) cc_final: 0.5996 (m-80) REVERT: D 950 GLN cc_start: 0.8386 (mm-40) cc_final: 0.7281 (pt0) REVERT: D 978 TYR cc_start: 0.6313 (m-80) cc_final: 0.5622 (m-80) REVERT: E 546 ILE cc_start: 0.7974 (mm) cc_final: 0.7719 (mm) REVERT: F 1043 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8080 (pt) outliers start: 19 outliers final: 16 residues processed: 271 average time/residue: 0.3920 time to fit residues: 165.4055 Evaluate side-chains 277 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 260 time to evaluate : 2.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain F residue 572 ASP 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 232 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 307 optimal weight: 0.9980 chunk 142 optimal weight: 0.5980 chunk 227 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.164851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.127662 restraints weight = 34474.329| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 2.97 r_work: 0.3148 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.158 25384 Z= 0.139 Angle : 0.708 59.077 34339 Z= 0.388 Chirality : 0.044 0.944 3891 Planarity : 0.004 0.057 4343 Dihedral : 7.246 93.951 3538 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.24 % Favored : 94.69 % Rotamer: Outliers : 0.63 % Allowed : 12.99 % Favored : 86.38 % 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: -0.13 (0.16), residues: 3128 helix: 1.31 (0.15), residues: 1370 sheet: -0.38 (0.24), residues: 462 loop : -1.52 (0.17), residues: 1296 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 0.022 0.001 PHE C 960 TYR 0.016 0.001 TYR C 978 ARG 0.004 0.000 ARG A 681 Details of bonding type rmsd hydrogen bonds : bond 0.02909 ( 1016) hydrogen bonds : angle 4.22166 ( 2970) SS BOND : bond 0.00251 ( 4) SS BOND : angle 1.89840 ( 8) covalent geometry : bond 0.00307 (25377) covalent geometry : angle 0.70751 (34331) Misc. bond : bond 0.00181 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11392.70 seconds wall clock time: 196 minutes 28.54 seconds (11788.54 seconds total)