Starting phenix.real_space_refine on Thu Mar 5 20:03:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sxo_25502/03_2026/7sxo_25502.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxo_25502/03_2026/7sxo_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 { model { file = "/net/cci-nas-00/data/ceres_data/7sxo_25502/03_2026/7sxo_25502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxo_25502/03_2026/7sxo_25502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sxo_25502/03_2026/7sxo_25502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxo_25502/03_2026/7sxo_25502.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 1, 'TYR: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: {'HIS:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1} 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: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU: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: 6.13, per 1000 atoms: 0.25 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: 2.18 Conformation dependent library (CDL) restraints added in 1.0 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: 0.84 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: 3.68 Time building geometry restraints manager: 2.88 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.070 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.050 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.780 ------------------------------------------------------------------------------- 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 : 8.43 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.000 ARG D 533 TYR 0.014 0.001 TYR D 812 PHE 0.015 0.001 PHE C1024 TRP 0.021 0.001 TRP C 934 HIS 0.005 0.001 HIS A 957 Details of bonding type rmsd covalent geometry : bond 0.00243 (25377) covalent geometry : angle 0.64909 (34331) SS BOND : bond 0.00384 ( 4) SS BOND : angle 2.11977 ( 8) hydrogen bonds : bond 0.16020 ( 1016) hydrogen bonds : angle 6.59544 ( 2970) 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 : 0.836 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: 0.4601 (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: 0.5902 (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: 0.1780 time to fit residues: 90.0192 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 : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 750 ASN A 798 HIS B1078 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN D 693 ASN D 726 ASN E 693 ASN E 725 GLN F 569 ASN F 693 ASN F 798 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.166321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128913 restraints weight = 34656.124| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.15 r_work: 0.3166 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 25384 Z= 0.120 Angle : 0.573 9.905 34339 Z= 0.287 Chirality : 0.042 0.192 3891 Planarity : 0.005 0.062 4343 Dihedral : 8.056 114.594 3538 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.02 % Favored : 94.85 % Rotamer: Outliers : 0.45 % Allowed : 6.53 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3128 helix: 0.87 (0.15), residues: 1367 sheet: -0.42 (0.24), residues: 463 loop : -1.59 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1064 TYR 0.016 0.001 TYR B 978 PHE 0.021 0.001 PHE C 613 TRP 0.012 0.001 TRP C 934 HIS 0.006 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00275 (25377) covalent geometry : angle 0.57270 (34331) SS BOND : bond 0.00176 ( 4) SS BOND : angle 1.42673 ( 8) hydrogen bonds : bond 0.03486 ( 1016) hydrogen bonds : angle 4.87074 ( 2970) Misc. bond : bond 0.00206 ( 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 304 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 292 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5517 (m-10) cc_final: 0.5187 (m-10) REVERT: B 649 LEU cc_start: 0.6799 (tp) cc_final: 0.6063 (mt) REVERT: B 801 MET cc_start: 0.8548 (mmm) cc_final: 0.8336 (mmm) REVERT: C 626 LYS cc_start: 0.7277 (tmtt) cc_final: 0.6882 (tmtt) REVERT: C 763 MET cc_start: 0.6788 (OUTLIER) cc_final: 0.6106 (tpt) REVERT: C 810 MET cc_start: 0.6950 (ppp) cc_final: 0.6041 (ttt) REVERT: C 827 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8262 (mt-10) REVERT: D 725 GLN cc_start: 0.7701 (mt0) cc_final: 0.7431 (mm-40) REVERT: D 798 HIS cc_start: 0.5938 (m90) cc_final: 0.5239 (m170) REVERT: D 920 LEU cc_start: 0.4971 (mp) cc_final: 0.3294 (tt) REVERT: D 978 TYR cc_start: 0.6073 (m-80) cc_final: 0.5610 (m-80) REVERT: E 546 ILE cc_start: 0.7796 (mm) cc_final: 0.7554 (mm) REVERT: E 568 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7584 (ttp80) REVERT: F 904 LYS cc_start: 0.8836 (ptmm) cc_final: 0.8561 (tmmt) outliers start: 12 outliers final: 5 residues processed: 299 average time/residue: 0.1737 time to fit residues: 79.9960 Evaluate side-chains 270 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 264 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 816 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 272 optimal weight: 8.9990 chunk 243 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 308 optimal weight: 0.0970 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 C 710 HIS ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN E 670 HIS E 725 GLN F 582 HIS ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.163099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125111 restraints weight = 34579.988| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 3.25 r_work: 0.3111 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25384 Z= 0.151 Angle : 0.579 9.305 34339 Z= 0.289 Chirality : 0.042 0.168 3891 Planarity : 0.005 0.060 4343 Dihedral : 7.870 110.809 3538 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.31 % Favored : 94.60 % Rotamer: Outliers : 0.82 % Allowed : 8.98 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 3128 helix: 0.94 (0.14), residues: 1369 sheet: -0.42 (0.24), residues: 469 loop : -1.61 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1056 TYR 0.021 0.001 TYR C 978 PHE 0.035 0.002 PHE C 960 TRP 0.013 0.001 TRP C 934 HIS 0.006 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00362 (25377) covalent geometry : angle 0.57828 (34331) SS BOND : bond 0.00224 ( 4) SS BOND : angle 1.65200 ( 8) hydrogen bonds : bond 0.03546 ( 1016) hydrogen bonds : angle 4.63141 ( 2970) Misc. bond : bond 0.00217 ( 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 297 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 275 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5929 (m-10) cc_final: 0.5193 (m-10) REVERT: C 661 MET cc_start: 0.3032 (tmm) cc_final: 0.2759 (ttp) REVERT: C 810 MET cc_start: 0.6915 (ppp) cc_final: 0.6241 (ttt) REVERT: C 827 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8274 (mt-10) REVERT: D 725 GLN cc_start: 0.7882 (mt0) cc_final: 0.7308 (mm-40) REVERT: D 798 HIS cc_start: 0.5882 (m90) cc_final: 0.5146 (m170) REVERT: D 920 LEU cc_start: 0.5200 (mp) cc_final: 0.3347 (tt) REVERT: D 978 TYR cc_start: 0.6328 (m-80) cc_final: 0.5741 (m-80) REVERT: E 546 ILE cc_start: 0.7796 (mm) cc_final: 0.7514 (mm) REVERT: E 568 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7493 (ttp80) REVERT: E 937 MET cc_start: 0.8265 (tmm) cc_final: 0.8024 (tmm) REVERT: F 904 LYS cc_start: 0.8856 (ptmm) cc_final: 0.8597 (tmmt) outliers start: 22 outliers final: 8 residues processed: 290 average time/residue: 0.1810 time to fit residues: 80.7562 Evaluate side-chains 263 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 255 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 296 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 289 optimal weight: 0.1980 chunk 288 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 190 optimal weight: 0.9990 chunk 1 optimal weight: 50.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 GLN ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN D 693 ASN F 582 HIS ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.162411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124005 restraints weight = 34462.204| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.22 r_work: 0.3113 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25384 Z= 0.150 Angle : 0.581 9.937 34339 Z= 0.288 Chirality : 0.043 0.179 3891 Planarity : 0.004 0.060 4343 Dihedral : 7.741 107.389 3538 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.50 % Favored : 94.41 % Rotamer: Outliers : 0.97 % Allowed : 10.88 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 3128 helix: 1.00 (0.14), residues: 1370 sheet: -0.43 (0.24), residues: 457 loop : -1.64 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1056 TYR 0.023 0.001 TYR C 978 PHE 0.034 0.002 PHE C 960 TRP 0.013 0.001 TRP C 934 HIS 0.005 0.001 HIS A 798 Details of bonding type rmsd covalent geometry : bond 0.00360 (25377) covalent geometry : angle 0.58009 (34331) SS BOND : bond 0.00218 ( 4) SS BOND : angle 1.86536 ( 8) hydrogen bonds : bond 0.03399 ( 1016) hydrogen bonds : angle 4.48493 ( 2970) Misc. bond : bond 0.00226 ( 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 296 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 270 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 573 TRP cc_start: 0.8325 (m100) cc_final: 0.8112 (m100) REVERT: A 674 TYR cc_start: 0.5796 (m-80) cc_final: 0.5323 (m-80) REVERT: A 719 GLU cc_start: 0.8610 (pp20) cc_final: 0.8368 (pp20) REVERT: A 960 PHE cc_start: 0.6098 (m-10) cc_final: 0.5440 (m-10) REVERT: C 661 MET cc_start: 0.2904 (tmm) cc_final: 0.2628 (ttp) REVERT: C 810 MET cc_start: 0.6801 (ppp) cc_final: 0.6285 (ttt) REVERT: C 827 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8337 (mt-10) REVERT: D 725 GLN cc_start: 0.7970 (mt0) cc_final: 0.7282 (mm-40) REVERT: D 978 TYR cc_start: 0.6516 (m-80) cc_final: 0.5922 (m-80) REVERT: E 546 ILE cc_start: 0.7843 (mm) cc_final: 0.7575 (mm) REVERT: E 568 ARG cc_start: 0.8169 (ttp-110) cc_final: 0.7493 (ttp80) REVERT: E 937 MET cc_start: 0.8238 (tmm) cc_final: 0.7967 (tmm) REVERT: F 904 LYS cc_start: 0.8864 (ptmm) cc_final: 0.8637 (tmmt) outliers start: 26 outliers final: 11 residues processed: 288 average time/residue: 0.1802 time to fit residues: 79.1099 Evaluate side-chains 265 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 254 time to evaluate : 0.921 ------------------------------------------------------------------------------- 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 970 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 237 optimal weight: 7.9990 chunk 150 optimal weight: 30.0000 chunk 26 optimal weight: 3.9990 chunk 243 optimal weight: 2.9990 chunk 251 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 253 optimal weight: 2.9990 chunk 212 optimal weight: 0.9980 chunk 157 optimal weight: 0.3980 chunk 74 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN D 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 = 0.3986 r_free = 0.3986 target = 0.162722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.124980 restraints weight = 34530.766| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 3.48 r_work: 0.3132 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25384 Z= 0.131 Angle : 0.571 9.478 34339 Z= 0.283 Chirality : 0.042 0.160 3891 Planarity : 0.004 0.060 4343 Dihedral : 7.653 105.465 3538 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.47 % Favored : 94.44 % Rotamer: Outliers : 1.00 % Allowed : 11.80 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.15), residues: 3128 helix: 1.05 (0.14), residues: 1377 sheet: -0.46 (0.24), residues: 457 loop : -1.64 (0.17), residues: 1294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1056 TYR 0.023 0.001 TYR C 978 PHE 0.035 0.001 PHE C 960 TRP 0.013 0.001 TRP C 934 HIS 0.004 0.001 HIS F 798 Details of bonding type rmsd covalent geometry : bond 0.00310 (25377) covalent geometry : angle 0.57018 (34331) SS BOND : bond 0.00220 ( 4) SS BOND : angle 2.09425 ( 8) hydrogen bonds : bond 0.03225 ( 1016) hydrogen bonds : angle 4.41548 ( 2970) Misc. bond : bond 0.00215 ( 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 292 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 265 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 672 ARG cc_start: 0.6768 (mmm160) cc_final: 0.6396 (mmm160) REVERT: A 719 GLU cc_start: 0.8441 (pp20) cc_final: 0.8227 (pp20) REVERT: A 960 PHE cc_start: 0.5820 (m-10) cc_final: 0.5297 (m-10) REVERT: A 983 MET cc_start: 0.8865 (tpt) cc_final: 0.8512 (tpt) REVERT: B 591 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7486 (ttp80) REVERT: C 661 MET cc_start: 0.2838 (tmm) cc_final: 0.2611 (ttp) REVERT: C 810 MET cc_start: 0.6719 (ppp) cc_final: 0.6193 (ttt) REVERT: C 827 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8373 (mt-10) REVERT: D 725 GLN cc_start: 0.7982 (mt0) cc_final: 0.7338 (mm-40) REVERT: D 978 TYR cc_start: 0.6491 (m-80) cc_final: 0.5840 (m-80) REVERT: E 546 ILE cc_start: 0.7866 (mm) cc_final: 0.7592 (mm) REVERT: E 568 ARG cc_start: 0.8121 (ttp-110) cc_final: 0.7484 (ttp80) REVERT: E 718 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8435 (mp) REVERT: E 937 MET cc_start: 0.8275 (tmm) cc_final: 0.7987 (tmm) REVERT: F 904 LYS cc_start: 0.8868 (ptmm) cc_final: 0.8657 (tmmt) REVERT: F 1043 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8154 (pt) outliers start: 27 outliers final: 14 residues processed: 280 average time/residue: 0.1826 time to fit residues: 78.2146 Evaluate side-chains 272 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 255 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain C residue 1039 MET Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain F residue 572 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 32 optimal weight: 0.2980 chunk 131 optimal weight: 0.0770 chunk 119 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 190 optimal weight: 0.8980 chunk 310 optimal weight: 0.9980 chunk 87 optimal weight: 1.9990 chunk 296 optimal weight: 4.9990 chunk 252 optimal weight: 7.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 586 GLN C 821 ASN D 693 ASN F 569 ASN ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.164489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.126928 restraints weight = 34454.110| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.08 r_work: 0.3146 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1653 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= 0.107 Angle : 0.556 11.271 34339 Z= 0.275 Chirality : 0.041 0.174 3891 Planarity : 0.004 0.060 4343 Dihedral : 7.507 102.932 3538 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 1.19 % Allowed : 11.95 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3128 helix: 1.18 (0.15), residues: 1377 sheet: -0.58 (0.24), residues: 470 loop : -1.58 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1051 TYR 0.015 0.001 TYR C 978 PHE 0.016 0.001 PHE D 653 TRP 0.015 0.001 TRP A 573 HIS 0.004 0.000 HIS F 798 Details of bonding type rmsd covalent geometry : bond 0.00242 (25377) covalent geometry : angle 0.55471 (34331) SS BOND : bond 0.01081 ( 4) SS BOND : angle 2.48094 ( 8) hydrogen bonds : bond 0.02973 ( 1016) hydrogen bonds : angle 4.33087 ( 2970) Misc. bond : bond 0.00195 ( 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 298 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 266 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 582 HIS cc_start: 0.7542 (m170) cc_final: 0.7175 (m170) REVERT: A 719 GLU cc_start: 0.8465 (pp20) cc_final: 0.8198 (pp20) REVERT: A 798 HIS cc_start: 0.4185 (m90) cc_final: 0.3476 (m-70) REVERT: A 960 PHE cc_start: 0.5884 (m-10) cc_final: 0.5269 (m-10) REVERT: A 983 MET cc_start: 0.8855 (tpt) cc_final: 0.8461 (tpt) REVERT: B 591 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7456 (ttp80) REVERT: C 810 MET cc_start: 0.6539 (ppp) cc_final: 0.6232 (ttt) REVERT: C 978 TYR cc_start: 0.6622 (m-10) cc_final: 0.6112 (m-80) REVERT: D 816 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6112 (pp20) REVERT: D 978 TYR cc_start: 0.6398 (m-80) cc_final: 0.5749 (m-80) REVERT: E 546 ILE cc_start: 0.7953 (mm) cc_final: 0.7668 (mm) REVERT: E 718 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8411 (mp) REVERT: E 937 MET cc_start: 0.8208 (tmm) cc_final: 0.7908 (tmm) REVERT: F 1043 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8152 (pt) outliers start: 32 outliers final: 17 residues processed: 286 average time/residue: 0.1768 time to fit residues: 77.9337 Evaluate side-chains 270 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 961 GLU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 1039 MET Chi-restraints excluded: chain D residue 747 CYS Chi-restraints excluded: chain D residue 816 GLU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain F residue 569 ASN 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 1043 LEU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 139 optimal weight: 0.1980 chunk 5 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 278 optimal weight: 0.6980 chunk 279 optimal weight: 0.0170 chunk 246 optimal weight: 0.0870 chunk 33 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 280 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS B 726 ASN B 821 ASN C 586 GLN C 798 HIS ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN F 569 ASN ** 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 = 0.4014 r_free = 0.4014 target = 0.165206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127594 restraints weight = 34240.029| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.24 r_work: 0.3163 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25384 Z= 0.107 Angle : 0.555 9.769 34339 Z= 0.275 Chirality : 0.041 0.254 3891 Planarity : 0.004 0.059 4343 Dihedral : 7.389 100.540 3538 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.76 % Rotamer: Outliers : 1.11 % Allowed : 12.77 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.16), residues: 3128 helix: 1.23 (0.15), residues: 1376 sheet: -0.52 (0.24), residues: 472 loop : -1.56 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 681 TYR 0.015 0.001 TYR C 978 PHE 0.017 0.001 PHE D 653 TRP 0.016 0.001 TRP C 934 HIS 0.004 0.000 HIS F 798 Details of bonding type rmsd covalent geometry : bond 0.00241 (25377) covalent geometry : angle 0.55362 (34331) SS BOND : bond 0.00303 ( 4) SS BOND : angle 2.26002 ( 8) hydrogen bonds : bond 0.02881 ( 1016) hydrogen bonds : angle 4.28076 ( 2970) Misc. bond : bond 0.00177 ( 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 294 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 719 GLU cc_start: 0.8462 (pp20) cc_final: 0.8183 (pp20) REVERT: A 798 HIS cc_start: 0.4039 (m90) cc_final: 0.2432 (m90) REVERT: A 960 PHE cc_start: 0.5854 (m-10) cc_final: 0.5219 (m-10) REVERT: A 983 MET cc_start: 0.8841 (tpt) cc_final: 0.8416 (tpt) REVERT: B 591 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7487 (ttp80) REVERT: C 978 TYR cc_start: 0.6638 (m-10) cc_final: 0.5783 (m-80) REVERT: D 978 TYR cc_start: 0.6328 (m-80) cc_final: 0.5659 (m-80) REVERT: E 546 ILE cc_start: 0.7896 (mm) cc_final: 0.7628 (mm) REVERT: E 718 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8375 (mp) REVERT: E 937 MET cc_start: 0.8191 (tmm) cc_final: 0.7877 (tmm) REVERT: F 1043 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8105 (pt) outliers start: 30 outliers final: 17 residues processed: 283 average time/residue: 0.1784 time to fit residues: 78.2686 Evaluate side-chains 277 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 257 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 1039 MET Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 718 LEU Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain F residue 569 ASN Chi-restraints excluded: chain F residue 702 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 917 THR Chi-restraints excluded: chain F residue 1043 LEU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 191 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 257 optimal weight: 0.8980 chunk 214 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN E 693 ASN ** F 569 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 = 0.3995 r_free = 0.3995 target = 0.163557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.125774 restraints weight = 34277.163| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.25 r_work: 0.3158 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25384 Z= 0.121 Angle : 0.569 10.208 34339 Z= 0.281 Chirality : 0.042 0.242 3891 Planarity : 0.004 0.058 4343 Dihedral : 7.358 98.875 3538 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 0.93 % Allowed : 13.25 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.15), residues: 3128 helix: 1.22 (0.15), residues: 1376 sheet: -0.54 (0.24), residues: 471 loop : -1.55 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 681 TYR 0.016 0.001 TYR C 978 PHE 0.018 0.001 PHE D 653 TRP 0.016 0.001 TRP C 934 HIS 0.008 0.001 HIS C 798 Details of bonding type rmsd covalent geometry : bond 0.00285 (25377) covalent geometry : angle 0.56782 (34331) SS BOND : bond 0.00303 ( 4) SS BOND : angle 2.08048 ( 8) hydrogen bonds : bond 0.02975 ( 1016) hydrogen bonds : angle 4.27226 ( 2970) Misc. bond : bond 0.00183 ( 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 289 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 264 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 GLU cc_start: 0.8490 (pp20) cc_final: 0.8165 (pp20) REVERT: A 960 PHE cc_start: 0.5754 (m-10) cc_final: 0.5290 (m-10) REVERT: A 983 MET cc_start: 0.8867 (tpt) cc_final: 0.8428 (tpt) REVERT: B 591 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.7442 (ttp80) REVERT: D 688 LYS cc_start: 0.7719 (mptt) cc_final: 0.7512 (mptt) REVERT: D 816 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6082 (pp20) REVERT: D 950 GLN cc_start: 0.8373 (mm-40) cc_final: 0.7250 (pt0) REVERT: D 978 TYR cc_start: 0.6353 (m-80) cc_final: 0.5660 (m-80) REVERT: E 546 ILE cc_start: 0.7904 (mm) cc_final: 0.7644 (mm) REVERT: E 937 MET cc_start: 0.8193 (tmm) cc_final: 0.7869 (tmm) REVERT: F 1043 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8092 (pt) outliers start: 25 outliers final: 17 residues processed: 280 average time/residue: 0.1694 time to fit residues: 72.9146 Evaluate side-chains 277 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 257 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 1039 MET Chi-restraints excluded: chain D residue 693 ASN Chi-restraints excluded: chain D residue 816 GLU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 957 HIS 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 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 270 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 59 optimal weight: 0.1980 chunk 256 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 276 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 181 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 693 ASN ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.3996 r_free = 0.3996 target = 0.163687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.126027 restraints weight = 34391.980| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.99 r_work: 0.3117 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25384 Z= 0.131 Angle : 0.580 10.825 34339 Z= 0.286 Chirality : 0.042 0.234 3891 Planarity : 0.004 0.058 4343 Dihedral : 7.366 96.743 3538 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.27 % Favored : 94.63 % Rotamer: Outliers : 1.04 % Allowed : 13.55 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 3128 helix: 1.22 (0.15), residues: 1375 sheet: -0.57 (0.24), residues: 472 loop : -1.55 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1051 TYR 0.016 0.001 TYR C 978 PHE 0.023 0.001 PHE C 960 TRP 0.018 0.001 TRP C 934 HIS 0.008 0.001 HIS C 798 Details of bonding type rmsd covalent geometry : bond 0.00312 (25377) covalent geometry : angle 0.57933 (34331) SS BOND : bond 0.00293 ( 4) SS BOND : angle 2.09227 ( 8) hydrogen bonds : bond 0.03065 ( 1016) hydrogen bonds : angle 4.28976 ( 2970) Misc. bond : bond 0.00180 ( 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 292 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 GLU cc_start: 0.8505 (pp20) cc_final: 0.8174 (pp20) REVERT: A 798 HIS cc_start: 0.4312 (m90) cc_final: 0.3029 (m-70) REVERT: A 960 PHE cc_start: 0.5931 (m-10) cc_final: 0.5436 (m-10) REVERT: A 983 MET cc_start: 0.8911 (tpt) cc_final: 0.8480 (tpt) REVERT: D 816 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6260 (pp20) REVERT: D 950 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7266 (pt0) REVERT: D 978 TYR cc_start: 0.6438 (m-80) cc_final: 0.5727 (m-80) REVERT: E 546 ILE cc_start: 0.7911 (mm) cc_final: 0.7656 (mm) REVERT: E 937 MET cc_start: 0.8199 (tmm) cc_final: 0.7893 (tmm) REVERT: F 1043 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8126 (pt) outliers start: 28 outliers final: 18 residues processed: 282 average time/residue: 0.1739 time to fit residues: 76.1841 Evaluate side-chains 282 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 718 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 961 GLU Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 1039 MET Chi-restraints excluded: chain D residue 816 GLU Chi-restraints excluded: chain D residue 970 MET 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 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 21 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 169 optimal weight: 0.6980 chunk 284 optimal weight: 3.9990 chunk 264 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN D 693 ASN F 569 ASN ** 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 = 0.3972 r_free = 0.3972 target = 0.161599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.123905 restraints weight = 34551.764| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 3.12 r_work: 0.3082 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1964 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= 0.169 Angle : 0.621 11.901 34339 Z= 0.308 Chirality : 0.043 0.232 3891 Planarity : 0.004 0.057 4343 Dihedral : 7.492 94.555 3538 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 1.00 % Allowed : 13.81 % Favored : 85.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 3128 helix: 1.10 (0.14), residues: 1381 sheet: -0.53 (0.24), residues: 457 loop : -1.66 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 655 TYR 0.022 0.001 TYR C 978 PHE 0.027 0.002 PHE C 960 TRP 0.019 0.001 TRP C 934 HIS 0.007 0.001 HIS C 798 Details of bonding type rmsd covalent geometry : bond 0.00409 (25377) covalent geometry : angle 0.62032 (34331) SS BOND : bond 0.00333 ( 4) SS BOND : angle 2.33636 ( 8) hydrogen bonds : bond 0.03416 ( 1016) hydrogen bonds : angle 4.38675 ( 2970) Misc. bond : bond 0.00133 ( 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 299 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 719 GLU cc_start: 0.8497 (pp20) cc_final: 0.8167 (pp20) REVERT: A 798 HIS cc_start: 0.4635 (m90) cc_final: 0.3369 (m-70) REVERT: A 960 PHE cc_start: 0.6004 (m-10) cc_final: 0.5457 (m-10) REVERT: B 763 MET cc_start: 0.3544 (ttp) cc_final: 0.3340 (ttp) REVERT: C 960 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.4676 (m-80) REVERT: C 978 TYR cc_start: 0.6481 (m-10) cc_final: 0.6044 (m-80) REVERT: D 816 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6203 (pp20) REVERT: D 950 GLN cc_start: 0.8445 (mm-40) cc_final: 0.7244 (pt0) REVERT: D 978 TYR cc_start: 0.6621 (m-80) cc_final: 0.5916 (m-80) REVERT: E 546 ILE cc_start: 0.8020 (mm) cc_final: 0.7764 (mm) REVERT: E 937 MET cc_start: 0.8148 (tmm) cc_final: 0.7821 (tmm) REVERT: E 1039 MET cc_start: 0.9189 (ptm) cc_final: 0.8954 (ptm) REVERT: F 1043 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8220 (pt) outliers start: 27 outliers final: 19 residues processed: 290 average time/residue: 0.1668 time to fit residues: 75.5090 Evaluate side-chains 282 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 718 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 961 GLU 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 C residue 960 PHE Chi-restraints excluded: chain C residue 1039 MET Chi-restraints excluded: chain D residue 693 ASN Chi-restraints excluded: chain D residue 816 GLU Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain F residue 569 ASN 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 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 15 optimal weight: 1.9990 chunk 272 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 285 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 283 optimal weight: 0.7980 chunk 150 optimal weight: 20.0000 chunk 201 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 178 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 HIS ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 586 GLN ** 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 = 0.3967 r_free = 0.3967 target = 0.161115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.123570 restraints weight = 34103.124| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 3.07 r_work: 0.3088 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.168 25384 Z= 0.256 Angle : 1.032 59.195 34339 Z= 0.614 Chirality : 0.049 0.884 3891 Planarity : 0.005 0.094 4343 Dihedral : 7.559 94.506 3538 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.79 % Favored : 94.12 % Rotamer: Outliers : 0.85 % Allowed : 13.99 % Favored : 85.15 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3128 helix: 1.07 (0.14), residues: 1381 sheet: -0.54 (0.24), residues: 457 loop : -1.66 (0.17), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 651 TYR 0.022 0.001 TYR C 978 PHE 0.030 0.002 PHE C 960 TRP 0.017 0.001 TRP C 934 HIS 0.007 0.001 HIS C 798 Details of bonding type rmsd covalent geometry : bond 0.00500 (25377) covalent geometry : angle 1.03148 (34331) SS BOND : bond 0.00589 ( 4) SS BOND : angle 2.39952 ( 8) hydrogen bonds : bond 0.03487 ( 1016) hydrogen bonds : angle 4.40534 ( 2970) Misc. bond : bond 0.00148 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5219.42 seconds wall clock time: 90 minutes 31.57 seconds (5431.57 seconds total)