Starting phenix.real_space_refine on Sun Jul 5 02:36:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sxo_25502/07_2026/7sxo_25502.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sxo_25502/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sxo_25502/07_2026/7sxo_25502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sxo_25502/07_2026/7sxo_25502.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7sxo_25502/07_2026/7sxo_25502.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sxo_25502/07_2026/7sxo_25502.cif" model { file = "/net/cci-nas-00/data/ceres_data/7sxo_25502/07_2026/7sxo_25502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sxo_25502/07_2026/7sxo_25502.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 5.20, per 1000 atoms: 0.21 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: 1.93 Conformation dependent library (CDL) restraints added in 820.5 milliseconds 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: 0.53 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: 3.74 Time building geometry restraints manager: 2.45 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: 14571 24.88 - 49.77: 770 49.77 - 74.65: 66 74.65 - 99.53: 26 99.53 - 124.42: 2 Dihedral angle restraints: 15435 sinusoidal: 6291 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 15432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 3887 0.189 - 0.378: 3 0.378 - 0.568: 0 0.568 - 0.757: 0 0.757 - 0.946: 1 Chirality restraints: 3891 Sorted by residual: chirality pdb=" CA LEU F 920 " pdb=" N LEU F 920 " pdb=" C LEU F 920 " pdb=" CB LEU F 920 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.24e+01 chirality pdb=" CA ASN F 954 " pdb=" N ASN F 954 " pdb=" C ASN F 954 " pdb=" CB ASN F 954 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA ASN D 693 " pdb=" N ASN D 693 " pdb=" C ASN D 693 " pdb=" CB ASN D 693 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 3888 not shown) Planarity restraints: 4343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 757 " -0.055 5.00e-02 4.00e+02 8.37e-02 1.12e+01 pdb=" N PRO D 758 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO D 758 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 758 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 678 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO E 679 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 679 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO E 679 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO F 912 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO F 913 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO F 913 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 913 " -0.035 5.00e-02 4.00e+02 ... (remaining 4340 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 338 2.65 - 3.22: 23005 3.22 - 3.78: 37793 3.78 - 4.34: 52104 4.34 - 4.90: 85976 Nonbonded interactions: 199216 Sorted by model distance: nonbonded pdb=" O LEU F 920 " pdb=" CB LEU F 920 " model vdw 2.092 2.752 nonbonded pdb=" OD1 ASN D 750 " pdb="MG MG D1201 " model vdw 2.114 2.170 nonbonded pdb=" NH1 ARG C 651 " pdb=" O GLN C 692 " model vdw 2.139 3.120 nonbonded pdb=" OG SER B 946 " pdb=" OH TYR B 978 " model vdw 2.193 3.040 nonbonded pdb=" OG1 THR D1046 " pdb=" OH TYR E 921 " model vdw 2.206 3.040 ... (remaining 199211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 628 or (resid 629 and (name N or name CA or name C \ or name O or name CB )) or resid 630 through 637 or (resid 638 and (name N or na \ me CA or name C or name O or name CB )) or resid 639 through 702 or (resid 703 a \ nd (name N or name CA or name C or name O or name CB )) or resid 704 or resid 71 \ 2 through 761 or (resid 762 and (name N or name CA or name C or name O or name C \ B )) or resid 763 through 841 or resid 896 through 903 or (resid 904 and (name N \ or name CA or name C or name O or name CB )) or resid 905 or (resid 906 through \ 908 and (name N or name CA or name C or name O or name CB )) or resid 909 throu \ gh 917 or (resid 918 through 919 and (name N or name CA or name C or name O or n \ ame CB )) or resid 920 through 953 or (resid 957 through 958 and (name N or name \ CA or name C or name O or name CB )) or resid 959 through 1123 or (resid 1124 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1125 or (resid \ 1126 and (name N or name CA or name C or name O or name CB )) or resid 1127)) selection = (chain 'B' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 621 or (resid 622 and (name N or name CA or name C \ or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA or nam \ e C or name O or name CB )) or resid 625 through 628 or (resid 629 and (name N o \ r name CA or name C or name O or name CB )) or resid 630 through 704 or resid 71 \ 2 through 761 or (resid 762 and (name N or name CA or name C or name O or name C \ B )) or resid 763 through 905 or (resid 906 through 908 and (name N or name CA o \ r name C or name O or name CB )) or resid 909 through 917 or (resid 918 through \ 919 and (name N or name CA or name C or name O or name CB )) or resid 920 throug \ h 953 or (resid 957 through 958 and (name N or name CA or name C or name O or na \ me CB )) or resid 959 through 1030 or resid 1032 through 1123 or (resid 1124 and \ (name N or name CA or name C or name O or name CB )) or resid 1125 or (resid 11 \ 26 and (name N or name CA or name C or name O or name CB )) or resid 1127)) selection = (chain 'C' and (resid 585 through 621 or (resid 622 and (name N or name CA or na \ me C or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA o \ r name C or name O or name CB )) or resid 625 through 637 or (resid 638 and (nam \ e N or name CA or name C or name O or name CB )) or resid 639 through 702 or (re \ sid 703 and (name N or name CA or name C or name O or name CB )) or resid 704 or \ resid 712 through 761 or (resid 762 and (name N or name CA or name C or name O \ or name CB )) or resid 763 through 841 or resid 896 through 906 or (resid 907 th \ rough 908 and (name N or name CA or name C or name O or name CB )) or resid 909 \ through 917 or (resid 918 through 919 and (name N or name CA or name C or name O \ or name CB )) or resid 920 through 953 or (resid 957 through 958 and (name N or \ name CA or name C or name O or name CB )) or resid 959 through 1030 or resid 10 \ 32 through 1123 or (resid 1124 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1125 or (resid 1126 and (name N or name CA or name C or name O \ or name CB )) or resid 1127)) selection = (chain 'D' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 621 or (resid 622 and (name N or name CA or name C \ or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA or nam \ e C or name O or name CB )) or resid 625 through 628 or (resid 629 and (name N o \ r name CA or name C or name O or name CB )) or resid 630 through 637 or (resid 6 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 639 through \ 702 or (resid 703 and (name N or name CA or name C or name O or name CB )) or r \ esid 704 or resid 712 through 841 or resid 896 through 903 or (resid 904 and (na \ me N or name CA or name C or name O or name CB )) or resid 905 or (resid 906 thr \ ough 908 and (name N or name CA or name C or name O or name CB )) or resid 909 t \ hrough 917 or (resid 918 through 919 and (name N or name CA or name C or name O \ or name CB )) or resid 920 through 953 or (resid 957 through 958 and (name N or \ name CA or name C or name O or name CB )) or resid 959 through 1030 or resid 103 \ 2 through 1127)) selection = (chain 'E' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 621 or (resid 622 and (name N or name CA or name C \ or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA or nam \ e C or name O or name CB )) or resid 625 through 637 or (resid 638 and (name N o \ r name CA or name C or name O or name CB )) or resid 639 through 702 or (resid 7 \ 03 and (name N or name CA or name C or name O or name CB )) or resid 704 or resi \ d 712 through 761 or (resid 762 and (name N or name CA or name C or name O or na \ me CB )) or resid 763 through 841 or resid 896 through 903 or (resid 904 and (na \ me N or name CA or name C or name O or name CB )) or resid 905 or (resid 906 thr \ ough 908 and (name N or name CA or name C or name O or name CB )) or resid 909 t \ hrough 917 or (resid 918 through 919 and (name N or name CA or name C or name O \ or name CB )) or resid 920 through 953 or (resid 957 through 958 and (name N or \ name CA or name C or name O or name CB )) or resid 959 through 1030 or resid 103 \ 2 through 1123 or (resid 1124 and (name N or name CA or name C or name O or name \ CB )) or resid 1125 or (resid 1126 and (name N or name CA or name C or name O o \ r name CB )) or resid 1127)) selection = (chain 'F' and ((resid 585 and (name N or name CA or name C or name O or name CB \ )) or resid 586 or (resid 587 and (name N or name CA or name C or name O or nam \ e CB )) or resid 588 through 621 or (resid 622 and (name N or name CA or name C \ or name O or name CB )) or resid 623 or (resid 624 and (name N or name CA or nam \ e C or name O or name CB )) or resid 625 through 628 or (resid 629 and (name N o \ r name CA or name C or name O or name CB )) or resid 630 through 637 or (resid 6 \ 38 and (name N or name CA or name C or name O or name CB )) or resid 639 through \ 702 or (resid 703 and (name N or name CA or name C or name O or name CB )) or r \ esid 704 or resid 712 through 761 or (resid 762 and (name N or name CA or name C \ or name O or name CB )) or resid 763 through 903 or (resid 904 and (name N or n \ ame CA or name C or name O or name CB )) or resid 905 or (resid 906 through 908 \ and (name N or name CA or name C or name O or name CB )) or resid 909 through 95 \ 3 or (resid 957 through 958 and (name N or name CA or name C or name O or name C \ B )) or resid 959 through 1030 or resid 1032 through 1125 or (resid 1126 and (na \ me N or name CA or name C or name O or name CB )) or resid 1127)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.760 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.010 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 14.384 124.418 9533 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/Z covalent geometry : bond 0.00243 / 0.13 (25377) covalent geometry : angle 0.64909 / 0.38 (34331) SS BOND : bond 0.00384 / 0.15 ( 4) SS BOND : angle 2.11977 / 1.16 ( 8) hydrogen bonds : bond 0.16020 / 11.05 ( 1016) hydrogen bonds : angle 6.59544 / 4.70 ( 2970) Misc. bond : bond 0.00259 / 0.12 ( 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 : 0.881 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: 0.1612 time to fit residues: 81.4507 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 : 0.799 ------------------------------------------------------------------------------- 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... 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 = 0.166327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128733 restraints weight = 34654.224| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 3.41 r_work: 0.3184 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.0952 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 9.793 34339 Z= 0.286 Chirality : 0.042 0.195 3891 Planarity : 0.005 0.061 4343 Dihedral : 5.690 115.056 3414 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.05 % Favored : 94.82 % 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: 0.86 (0.15), residues: 1367 sheet: -0.43 (0.24), residues: 464 loop : -1.59 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1064 TYR 0.017 0.001 TYR B 978 PHE 0.021 0.001 PHE C 960 TRP 0.012 0.001 TRP C 934 HIS 0.006 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (25377) covalent geometry : angle 0.57226 / 0.29 (34331) SS BOND : bond 0.00184 / 0.08 ( 4) SS BOND : angle 1.39933 / 0.86 ( 8) hydrogen bonds : bond 0.03532 / 2.35 ( 1016) hydrogen bonds : angle 4.88476 / 3.47 ( 2970) Misc. bond : bond 0.00207 / 0.10 ( 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 : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 960 PHE cc_start: 0.5498 (m-10) cc_final: 0.5207 (m-10) REVERT: B 649 LEU cc_start: 0.6802 (tp) cc_final: 0.6072 (mt) REVERT: B 801 MET cc_start: 0.8550 (mmm) cc_final: 0.8339 (mmm) REVERT: C 626 LYS cc_start: 0.7247 (tmtt) cc_final: 0.6857 (tmtt) REVERT: C 763 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6116 (tpt) REVERT: C 810 MET cc_start: 0.6950 (ppp) cc_final: 0.6032 (ttt) REVERT: C 827 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8267 (mt-10) REVERT: D 725 GLN cc_start: 0.7697 (mt0) cc_final: 0.7405 (mm-40) REVERT: D 798 HIS cc_start: 0.5902 (m90) cc_final: 0.5201 (m170) REVERT: D 920 LEU cc_start: 0.4930 (mp) cc_final: 0.3281 (tt) REVERT: D 978 TYR cc_start: 0.6039 (m-80) cc_final: 0.5584 (m-80) REVERT: E 546 ILE cc_start: 0.7774 (mm) cc_final: 0.7537 (mm) REVERT: E 568 ARG cc_start: 0.8146 (ttp-110) cc_final: 0.7556 (ttp80) REVERT: E 816 GLU cc_start: 0.7694 (pm20) cc_final: 0.7415 (pm20) REVERT: F 904 LYS cc_start: 0.8833 (ptmm) cc_final: 0.8560 (tmmt) outliers start: 12 outliers final: 5 residues processed: 299 average time/residue: 0.1846 time to fit residues: 84.5317 Evaluate side-chains 272 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 266 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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: 0.3980 chunk 243 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 308 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1078 ASN C 710 HIS 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 = 0.3994 r_free = 0.3994 target = 0.163401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.125796 restraints weight = 34572.903| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.09 r_work: 0.3108 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25384 Z= 0.154 Angle : 0.579 9.322 34339 Z= 0.288 Chirality : 0.042 0.167 3891 Planarity : 0.005 0.060 4343 Dihedral : 5.716 111.310 3414 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.21 % Favored : 94.69 % Rotamer: Outliers : 0.85 % Allowed : 8.83 % Favored : 90.31 % 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: -0.47 (0.15), residues: 3128 helix: 0.93 (0.14), residues: 1369 sheet: -0.35 (0.24), residues: 458 loop : -1.65 (0.17), residues: 1301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E1056 TYR 0.021 0.001 TYR C 978 PHE 0.033 0.002 PHE C 960 TRP 0.012 0.001 TRP C 934 HIS 0.004 0.001 HIS F 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 (25377) covalent geometry : angle 0.57845 / 0.29 (34331) SS BOND : bond 0.00229 / 0.10 ( 4) SS BOND : angle 1.65339 / 0.99 ( 8) hydrogen bonds : bond 0.03557 / 2.35 ( 1016) hydrogen bonds : angle 4.64288 / 3.30 ( 2970) Misc. bond : bond 0.00212 / 0.10 ( 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 299 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 276 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 719 GLU cc_start: 0.8531 (pp20) cc_final: 0.8287 (pp20) REVERT: A 960 PHE cc_start: 0.5947 (m-10) cc_final: 0.5213 (m-10) REVERT: C 661 MET cc_start: 0.2902 (tmm) cc_final: 0.2659 (ttp) REVERT: C 827 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8247 (mt-10) REVERT: D 725 GLN cc_start: 0.7846 (mt0) cc_final: 0.7356 (mm-40) REVERT: D 798 HIS cc_start: 0.5835 (m90) cc_final: 0.5077 (m170) REVERT: D 920 LEU cc_start: 0.5198 (mp) cc_final: 0.3352 (tt) REVERT: D 978 TYR cc_start: 0.6368 (m-80) cc_final: 0.5767 (m-80) REVERT: E 546 ILE cc_start: 0.7855 (mm) cc_final: 0.7572 (mm) REVERT: E 568 ARG cc_start: 0.8206 (ttp-110) cc_final: 0.7533 (ttp80) REVERT: E 937 MET cc_start: 0.8262 (tmm) cc_final: 0.8014 (tmm) REVERT: F 753 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7885 (mm-30) REVERT: F 904 LYS cc_start: 0.8868 (ptmm) cc_final: 0.8611 (tmmt) outliers start: 23 outliers final: 9 residues processed: 292 average time/residue: 0.1856 time to fit residues: 84.0345 Evaluate side-chains 264 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 255 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 736 ILE 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: 0.0050 chunk 55 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 86 optimal weight: 0.1980 chunk 289 optimal weight: 0.0670 chunk 288 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 190 optimal weight: 0.9980 chunk 1 optimal weight: 50.0000 overall best weight: 0.4332 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 798 HIS B1078 ASN C 821 ASN C1078 ASN D 693 ASN E 670 HIS ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 582 HIS F 798 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.166514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.129148 restraints weight = 34421.769| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 3.07 r_work: 0.3175 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25384 Z= 0.097 Angle : 0.534 9.429 34339 Z= 0.264 Chirality : 0.041 0.178 3891 Planarity : 0.004 0.062 4343 Dihedral : 5.482 106.862 3414 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 0.97 % Allowed : 10.13 % Favored : 88.90 % 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 (0.16), residues: 3128 helix: 1.20 (0.15), residues: 1365 sheet: -0.45 (0.24), residues: 472 loop : -1.56 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 681 TYR 0.018 0.001 TYR C 978 PHE 0.023 0.001 PHE C 960 TRP 0.014 0.001 TRP C 934 HIS 0.006 0.001 HIS A 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (25377) covalent geometry : angle 0.53363 / 0.26 (34331) SS BOND : bond 0.00120 / 0.05 ( 4) SS BOND : angle 1.28415 / 0.76 ( 8) hydrogen bonds : bond 0.02856 / 1.88 ( 1016) hydrogen bonds : angle 4.34242 / 3.09 ( 2970) Misc. bond : bond 0.00188 / 0.09 ( 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 305 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 279 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 719 GLU cc_start: 0.8697 (pp20) cc_final: 0.8488 (pp20) REVERT: A 960 PHE cc_start: 0.5812 (m-10) cc_final: 0.5411 (m-10) REVERT: A 983 MET cc_start: 0.9051 (tpt) cc_final: 0.8833 (tpt) REVERT: C 661 MET cc_start: 0.2833 (tmm) cc_final: 0.2601 (ttp) REVERT: C 763 MET cc_start: 0.6645 (OUTLIER) cc_final: 0.5847 (tpt) REVERT: C 810 MET cc_start: 0.7014 (ppp) cc_final: 0.6208 (ttt) REVERT: C 827 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8262 (mt-10) REVERT: C 978 TYR cc_start: 0.6699 (m-80) cc_final: 0.5736 (m-80) REVERT: D 725 GLN cc_start: 0.7738 (mt0) cc_final: 0.7288 (mm-40) REVERT: D 798 HIS cc_start: 0.5704 (m90) cc_final: 0.5169 (m170) REVERT: D 978 TYR cc_start: 0.6147 (m-80) cc_final: 0.5522 (m-80) REVERT: E 546 ILE cc_start: 0.7878 (mm) cc_final: 0.7599 (mm) REVERT: E 568 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7538 (ttp80) REVERT: E 718 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8281 (mp) REVERT: E 937 MET cc_start: 0.8283 (tmm) cc_final: 0.8016 (tmm) REVERT: F 753 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7878 (mm-30) REVERT: F 904 LYS cc_start: 0.8885 (ptmm) cc_final: 0.8680 (tmmt) outliers start: 26 outliers final: 8 residues processed: 295 average time/residue: 0.1821 time to fit residues: 83.0153 Evaluate side-chains 264 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 254 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 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 E residue 718 LEU Chi-restraints excluded: chain E residue 957 HIS Chi-restraints excluded: chain F residue 572 ASP Chi-restraints excluded: chain F residue 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: 20.0000 chunk 26 optimal weight: 2.9990 chunk 243 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 253 optimal weight: 0.9990 chunk 212 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 74 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 903 GLN B1078 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 HIS C 821 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.162832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124703 restraints weight = 34543.176| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.14 r_work: 0.3148 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25384 Z= 0.156 Angle : 0.580 9.703 34339 Z= 0.287 Chirality : 0.042 0.169 3891 Planarity : 0.004 0.058 4343 Dihedral : 5.600 105.135 3414 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.31 % Favored : 94.60 % Rotamer: Outliers : 0.71 % Allowed : 11.40 % Favored : 87.90 % 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: -0.34 (0.15), residues: 3128 helix: 1.10 (0.14), residues: 1370 sheet: -0.35 (0.24), residues: 448 loop : -1.64 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E1064 TYR 0.019 0.001 TYR B 978 PHE 0.030 0.002 PHE C 960 TRP 0.013 0.001 TRP C 934 HIS 0.006 0.001 HIS F 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (25377) covalent geometry : angle 0.57964 / 0.29 (34331) SS BOND : bond 0.00233 / 0.11 ( 4) SS BOND : angle 2.10819 / 1.24 ( 8) hydrogen bonds : bond 0.03317 / 2.20 ( 1016) hydrogen bonds : angle 4.39209 / 3.13 ( 2970) Misc. bond : bond 0.00200 / 0.09 ( 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 284 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 265 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 674 TYR cc_start: 0.5604 (m-80) cc_final: 0.5188 (m-80) REVERT: A 719 GLU cc_start: 0.8589 (pp20) cc_final: 0.8363 (pp20) REVERT: A 960 PHE cc_start: 0.5740 (m-10) cc_final: 0.5279 (m-10) REVERT: A 983 MET cc_start: 0.9051 (tpt) cc_final: 0.8845 (tpt) REVERT: B 591 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7504 (ttp80) REVERT: C 827 GLU cc_start: 0.8470 (mt-10) cc_final: 0.8265 (mt-10) REVERT: D 725 GLN cc_start: 0.7843 (mt0) cc_final: 0.7275 (mm-40) REVERT: D 978 TYR cc_start: 0.6420 (m-80) cc_final: 0.5756 (m-80) REVERT: E 546 ILE cc_start: 0.7920 (mm) cc_final: 0.7633 (mm) REVERT: E 937 MET cc_start: 0.8277 (tmm) cc_final: 0.8014 (tmm) outliers start: 19 outliers final: 10 residues processed: 277 average time/residue: 0.1803 time to fit residues: 76.7759 Evaluate side-chains 264 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 253 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain D residue 970 MET Chi-restraints excluded: chain E residue 571 LEU Chi-restraints excluded: chain F residue 572 ASP Chi-restraints excluded: chain F residue 798 HIS Chi-restraints excluded: chain F residue 816 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 32 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 121 optimal weight: 0.0060 chunk 104 optimal weight: 0.9980 chunk 265 optimal weight: 4.9990 chunk 190 optimal weight: 0.8980 chunk 310 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 296 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1078 ASN C 586 GLN C 798 HIS C 821 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.164658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126927 restraints weight = 34446.907| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 3.02 r_work: 0.3131 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1644 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= 0.109 Angle : 0.555 12.131 34339 Z= 0.274 Chirality : 0.041 0.160 3891 Planarity : 0.004 0.060 4343 Dihedral : 5.539 102.954 3414 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 0.89 % Allowed : 11.66 % Favored : 87.45 % 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: -0.27 (0.15), residues: 3128 helix: 1.18 (0.14), residues: 1377 sheet: -0.47 (0.24), residues: 460 loop : -1.58 (0.17), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1051 TYR 0.020 0.001 TYR C 978 PHE 0.030 0.001 PHE C 960 TRP 0.014 0.001 TRP C 934 HIS 0.005 0.001 HIS F 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (25377) covalent geometry : angle 0.55332 / 0.27 (34331) SS BOND : bond 0.00902 / 0.34 ( 4) SS BOND : angle 3.02817 / 1.32 ( 8) hydrogen bonds : bond 0.03001 / 1.97 ( 1016) hydrogen bonds : angle 4.32373 / 3.08 ( 2970) Misc. bond : bond 0.00190 / 0.09 ( 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 294 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 270 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 672 ARG cc_start: 0.6701 (mmm160) cc_final: 0.6389 (mmm160) REVERT: A 719 GLU cc_start: 0.8595 (pp20) cc_final: 0.8336 (pp20) REVERT: A 960 PHE cc_start: 0.5917 (m-10) cc_final: 0.5353 (m-10) REVERT: A 983 MET cc_start: 0.9037 (tpt) cc_final: 0.8811 (tpt) REVERT: B 591 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7474 (ttp80) REVERT: C 810 MET cc_start: 0.7031 (ppp) cc_final: 0.6459 (ttt) REVERT: C 827 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8308 (mt-10) REVERT: D 725 GLN cc_start: 0.7823 (mt0) cc_final: 0.7262 (mm-40) REVERT: D 978 TYR cc_start: 0.6360 (m-80) cc_final: 0.5697 (m-80) REVERT: E 546 ILE cc_start: 0.7873 (mm) cc_final: 0.7579 (mm) REVERT: E 718 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8407 (mp) REVERT: E 937 MET cc_start: 0.8237 (tmm) cc_final: 0.7934 (tmm) REVERT: F 1043 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8166 (pt) outliers start: 24 outliers final: 16 residues processed: 283 average time/residue: 0.1846 time to fit residues: 80.3218 Evaluate side-chains 280 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 543 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain B residue 591 ARG Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 1078 ASN Chi-restraints excluded: chain C residue 744 LEU Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 821 ASN Chi-restraints excluded: chain D residue 747 CYS Chi-restraints excluded: chain D residue 922 GLU 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 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: 0.9980 chunk 5 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 278 optimal weight: 5.9990 chunk 279 optimal weight: 0.0170 chunk 246 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 72 optimal weight: 5.9990 chunk 280 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 overall best weight: 0.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 726 ASN B 821 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 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 = 0.4008 r_free = 0.4008 target = 0.164712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127301 restraints weight = 34287.446| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.98 r_work: 0.3140 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25384 Z= 0.111 Angle : 0.558 9.837 34339 Z= 0.275 Chirality : 0.041 0.246 3891 Planarity : 0.004 0.058 4343 Dihedral : 5.487 101.005 3414 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.27 % Favored : 94.63 % Rotamer: Outliers : 1.00 % Allowed : 12.32 % Favored : 86.67 % 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: -0.22 (0.15), residues: 3128 helix: 1.25 (0.15), residues: 1370 sheet: -0.47 (0.24), residues: 460 loop : -1.58 (0.17), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 681 TYR 0.020 0.001 TYR C 978 PHE 0.021 0.001 PHE C 960 TRP 0.015 0.001 TRP C 934 HIS 0.009 0.001 HIS C 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (25377) covalent geometry : angle 0.55684 / 0.27 (34331) SS BOND : bond 0.00290 / 0.11 ( 4) SS BOND : angle 2.41286 / 1.11 ( 8) hydrogen bonds : bond 0.02938 / 1.93 ( 1016) hydrogen bonds : angle 4.29013 / 3.05 ( 2970) Misc. bond : bond 0.00178 / 0.08 ( 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 290 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 263 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 719 GLU cc_start: 0.8610 (pp20) cc_final: 0.8343 (pp20) REVERT: A 960 PHE cc_start: 0.5855 (m-10) cc_final: 0.5284 (m-10) REVERT: A 983 MET cc_start: 0.9017 (tpt) cc_final: 0.8775 (tpt) REVERT: B 591 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7472 (ttp80) REVERT: C 978 TYR cc_start: 0.6656 (m-80) cc_final: 0.5837 (m-80) REVERT: D 978 TYR cc_start: 0.6324 (m-80) cc_final: 0.5660 (m-80) REVERT: E 546 ILE cc_start: 0.7950 (mm) cc_final: 0.7685 (mm) REVERT: E 937 MET cc_start: 0.8228 (tmm) cc_final: 0.7947 (tmm) REVERT: F 753 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7906 (mm-30) REVERT: F 1043 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8105 (pt) outliers start: 27 outliers final: 16 residues processed: 280 average time/residue: 0.1650 time to fit residues: 72.0382 Evaluate side-chains 274 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 256 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 920 LEU Chi-restraints excluded: chain D residue 922 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 798 HIS Chi-restraints excluded: chain F residue 816 GLU Chi-restraints excluded: chain F residue 1043 LEU Chi-restraints excluded: chain F residue 1110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 191 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 257 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 821 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 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 = 0.3997 r_free = 0.3997 target = 0.163728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.126282 restraints weight = 34309.791| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.04 r_work: 0.3137 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1758 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= 0.118 Angle : 0.570 10.287 34339 Z= 0.280 Chirality : 0.042 0.246 3891 Planarity : 0.004 0.057 4343 Dihedral : 5.470 99.259 3414 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.21 % Favored : 94.69 % Rotamer: Outliers : 1.00 % Allowed : 12.69 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.22 (0.15), residues: 3128 helix: 1.25 (0.15), residues: 1369 sheet: -0.47 (0.24), residues: 462 loop : -1.56 (0.17), residues: 1297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 681 TYR 0.018 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/Z covalent geometry : bond 0.00280 / 0.12 (25377) covalent geometry : angle 0.56939 / 0.28 (34331) SS BOND : bond 0.00303 / 0.12 ( 4) SS BOND : angle 2.24740 / 1.09 ( 8) hydrogen bonds : bond 0.02976 / 1.96 ( 1016) hydrogen bonds : angle 4.29220 / 3.05 ( 2970) Misc. bond : bond 0.00125 / 0.06 ( 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 290 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 263 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 719 GLU cc_start: 0.8596 (pp20) cc_final: 0.8290 (pp20) REVERT: A 960 PHE cc_start: 0.5781 (m-10) cc_final: 0.5271 (m-10) REVERT: A 983 MET cc_start: 0.9026 (tpt) cc_final: 0.8780 (tpt) REVERT: B 591 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7455 (ttp80) REVERT: C 661 MET cc_start: 0.2768 (tmm) cc_final: 0.1504 (ttp) REVERT: C 810 MET cc_start: 0.7082 (ppp) cc_final: 0.6475 (ttt) REVERT: C 978 TYR cc_start: 0.6669 (m-80) cc_final: 0.5824 (m-80) REVERT: D 816 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6105 (pp20) REVERT: D 950 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7261 (pt0) REVERT: D 978 TYR cc_start: 0.6338 (m-80) cc_final: 0.5662 (m-80) REVERT: E 546 ILE cc_start: 0.7959 (mm) cc_final: 0.7694 (mm) REVERT: E 718 LEU cc_start: 0.8450 (mp) cc_final: 0.8161 (mt) REVERT: E 937 MET cc_start: 0.8229 (tmm) cc_final: 0.7926 (tmm) REVERT: F 753 GLU cc_start: 0.8254 (mm-30) cc_final: 0.8008 (mm-30) REVERT: F 1043 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8102 (pt) outliers start: 27 outliers final: 16 residues processed: 282 average time/residue: 0.1668 time to fit residues: 72.8874 Evaluate side-chains 275 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 256 time to evaluate : 0.889 ------------------------------------------------------------------------------- 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 C residue 763 MET Chi-restraints excluded: chain D residue 816 GLU Chi-restraints excluded: chain D residue 920 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 270 optimal weight: 0.0870 chunk 20 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 256 optimal weight: 0.3980 chunk 184 optimal weight: 2.9990 chunk 276 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 181 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** 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 = 0.4008 r_free = 0.4008 target = 0.164695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.127377 restraints weight = 34417.032| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.04 r_work: 0.3136 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25384 Z= 0.113 Angle : 0.569 10.368 34339 Z= 0.279 Chirality : 0.042 0.238 3891 Planarity : 0.004 0.057 4343 Dihedral : 5.434 97.220 3414 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.73 % Rotamer: Outliers : 0.78 % Allowed : 13.03 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.18 (0.16), residues: 3128 helix: 1.28 (0.15), residues: 1370 sheet: -0.50 (0.24), residues: 471 loop : -1.52 (0.17), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1051 TYR 0.017 0.001 TYR C 978 PHE 0.018 0.001 PHE D 653 TRP 0.018 0.001 TRP C 934 HIS 0.008 0.001 HIS C 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 (25377) covalent geometry : angle 0.56775 / 0.28 (34331) SS BOND : bond 0.00286 / 0.11 ( 4) SS BOND : angle 2.11127 / 1.05 ( 8) hydrogen bonds : bond 0.02920 / 1.92 ( 1016) hydrogen bonds : angle 4.26004 / 3.03 ( 2970) Misc. bond : bond 0.00109 / 0.05 ( 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 280 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 259 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 719 GLU cc_start: 0.8605 (pp20) cc_final: 0.8317 (pp20) REVERT: A 798 HIS cc_start: 0.4353 (m90) cc_final: 0.3054 (m-70) REVERT: A 960 PHE cc_start: 0.5788 (m-10) cc_final: 0.5287 (m-10) REVERT: A 983 MET cc_start: 0.9022 (tpt) cc_final: 0.8771 (tpt) REVERT: C 661 MET cc_start: 0.2850 (tmm) cc_final: 0.1542 (ttp) REVERT: C 810 MET cc_start: 0.7033 (ppp) cc_final: 0.6435 (ttt) REVERT: C 978 TYR cc_start: 0.6707 (m-80) cc_final: 0.5761 (m-80) REVERT: D 816 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6147 (pp20) REVERT: D 950 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7286 (pt0) REVERT: D 978 TYR cc_start: 0.6324 (m-80) cc_final: 0.5651 (m-80) REVERT: E 546 ILE cc_start: 0.7955 (mm) cc_final: 0.7681 (mm) REVERT: E 937 MET cc_start: 0.8210 (tmm) cc_final: 0.7910 (tmm) REVERT: F 753 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7961 (mm-30) REVERT: F 1043 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8100 (pt) outliers start: 21 outliers final: 15 residues processed: 273 average time/residue: 0.1884 time to fit residues: 79.3039 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 : 0.997 ------------------------------------------------------------------------------- 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 821 ASN 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 920 LEU 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 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: 6.9990 chunk 261 optimal weight: 20.0000 chunk 134 optimal weight: 3.9990 chunk 221 optimal weight: 0.5980 chunk 56 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 284 optimal weight: 0.9990 chunk 264 optimal weight: 0.0070 chunk 210 optimal weight: 0.9990 overall best weight: 0.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 GLN B 821 ASN B1078 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.165146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.127368 restraints weight = 34520.497| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.26 r_work: 0.3172 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 25384 Z= 0.107 Angle : 0.564 10.358 34339 Z= 0.277 Chirality : 0.041 0.236 3891 Planarity : 0.004 0.058 4343 Dihedral : 5.385 95.419 3414 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.99 % Favored : 94.92 % Rotamer: Outliers : 0.82 % Allowed : 13.10 % Favored : 86.08 % 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: -0.12 (0.16), residues: 3128 helix: 1.33 (0.15), residues: 1369 sheet: -0.47 (0.24), residues: 471 loop : -1.49 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 681 TYR 0.015 0.001 TYR C 978 PHE 0.019 0.001 PHE D 653 TRP 0.018 0.001 TRP C 934 HIS 0.007 0.001 HIS C 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (25377) covalent geometry : angle 0.56324 / 0.28 (34331) SS BOND : bond 0.00276 / 0.11 ( 4) SS BOND : angle 1.98600 / 1.00 ( 8) hydrogen bonds : bond 0.02850 / 1.87 ( 1016) hydrogen bonds : angle 4.22771 / 3.00 ( 2970) Misc. bond : bond 0.00177 / 0.08 ( 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 286 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 264 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 719 GLU cc_start: 0.8595 (pp20) cc_final: 0.8309 (pp20) REVERT: A 798 HIS cc_start: 0.4329 (m90) cc_final: 0.3086 (m-70) REVERT: A 960 PHE cc_start: 0.5684 (m-10) cc_final: 0.5212 (m-10) REVERT: A 983 MET cc_start: 0.9037 (tpt) cc_final: 0.8804 (tpt) REVERT: C 661 MET cc_start: 0.2956 (tmm) cc_final: 0.1587 (ttp) REVERT: C 810 MET cc_start: 0.7072 (ppp) cc_final: 0.6480 (ttt) REVERT: C 978 TYR cc_start: 0.6586 (m-80) cc_final: 0.5650 (m-80) REVERT: C 1056 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7778 (ttp80) REVERT: D 816 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6005 (pp20) REVERT: D 950 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7277 (pt0) REVERT: D 978 TYR cc_start: 0.6230 (m-80) cc_final: 0.5570 (m-80) REVERT: E 546 ILE cc_start: 0.7874 (mm) cc_final: 0.7614 (mm) REVERT: E 937 MET cc_start: 0.8106 (tmm) cc_final: 0.7770 (tmm) REVERT: F 753 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7933 (mm-30) REVERT: F 1043 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8083 (pt) outliers start: 22 outliers final: 17 residues processed: 279 average time/residue: 0.1829 time to fit residues: 79.1236 Evaluate side-chains 277 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 258 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 1078 ASN 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 920 LEU 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 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: 5.9990 chunk 272 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 285 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 283 optimal weight: 1.9990 chunk 150 optimal weight: 20.0000 chunk 201 optimal weight: 0.0070 chunk 5 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN ** C 586 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.164806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.126981 restraints weight = 34326.286| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.26 r_work: 0.3185 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.137 25384 Z= 0.167 Angle : 0.710 59.200 34339 Z= 0.393 Chirality : 0.044 0.904 3891 Planarity : 0.005 0.157 4343 Dihedral : 5.397 95.445 3414 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.96 % Favored : 94.95 % Rotamer: Outliers : 0.74 % Allowed : 13.18 % Favored : 86.08 % Cbeta Deviations : 0.07 % 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: -0.14 (0.16), residues: 3128 helix: 1.30 (0.15), residues: 1369 sheet: -0.46 (0.24), residues: 471 loop : -1.49 (0.18), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 681 TYR 0.014 0.001 TYR C 978 PHE 0.018 0.001 PHE D 653 TRP 0.017 0.001 TRP C 934 HIS 0.015 0.001 HIS C 798 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.17 (25377) covalent geometry : angle 0.70981 / 0.39 (34331) SS BOND : bond 0.00311 / 0.12 ( 4) SS BOND : angle 1.96040 / 0.99 ( 8) hydrogen bonds : bond 0.02898 / 1.90 ( 1016) hydrogen bonds : angle 4.22835 / 3.00 ( 2970) Misc. bond : bond 0.00173 / 0.08 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5146.84 seconds wall clock time: 89 minutes 32.28 seconds (5372.28 seconds total)