Starting phenix.real_space_refine on Thu Jun 19 21:35:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd9_37128/06_2025/8kd9_37128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd9_37128/06_2025/8kd9_37128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kd9_37128/06_2025/8kd9_37128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd9_37128/06_2025/8kd9_37128.map" model { file = "/net/cci-nas-00/data/ceres_data/8kd9_37128/06_2025/8kd9_37128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd9_37128/06_2025/8kd9_37128.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians P 360 5.49 5 S 41 5.16 5 C 13508 2.51 5 N 4256 2.21 5 O 5558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23723 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 906 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 5, 'TRANS': 175} Chain breaks: 2 Unresolved non-hydrogen bonds: 597 Unresolved non-hydrogen angles: 760 Unresolved non-hydrogen dihedrals: 490 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 12, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 2, 'PHE:plan': 10, 'GLU:plan': 20, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 349 Chain: "B" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 926 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 159} Link IDs: {'PTRANS': 5, 'TRANS': 179} Chain breaks: 1 Unresolved non-hydrogen bonds: 615 Unresolved non-hydrogen angles: 784 Unresolved non-hydrogen dihedrals: 505 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 10, 'GLU:plan': 22, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 364 Chain: "C" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1556 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "D" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "E" Number of atoms: 1551 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 188, 1543 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Conformer: "B" Number of residues, atoms: 188, 1543 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} bond proxies already assigned to first conformer: 1561 Chain: "F" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1556 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 5, 'TRANS': 183} Chain: "G" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1546 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 5, 'TRANS': 182} Chain: "H" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "I" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 5, 'TRANS': 181} Chain: "J" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1528 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 5, 'TRANS': 180} Chain breaks: 1 Chain: "K" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 911 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 5, 'TRANS': 176} Chain breaks: 1 Unresolved non-hydrogen bonds: 604 Unresolved non-hydrogen angles: 770 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 10, 'GLU:plan': 20, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 353 Chain: "L" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 892 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 153} Link IDs: {'PTRANS': 5, 'TRANS': 172} Chain breaks: 2 Unresolved non-hydrogen bonds: 593 Unresolved non-hydrogen angles: 756 Unresolved non-hydrogen dihedrals: 489 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 10, 'GLU:plan': 19, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 347 Chain: "T" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 5, 'rna3p_pur': 34, 'rna3p_pyr': 28} Link IDs: {'rna2p': 9, 'rna3p': 63} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 63} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 9, 'rna3p': 63} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "O" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 30} Link IDs: {'rna2p': 10, 'rna3p': 62} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "P" Number of atoms: 1547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1547 Classifications: {'DNA': 1, 'RNA': 72} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 3, 'rna3p_pur': 33, 'rna3p_pyr': 30} Link IDs: {'rna2p': 9, 'rna3p': 63} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan2': 1, ' A%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 16.51, per 1000 atoms: 0.70 Number of scatterers: 23723 At special positions: 0 Unit cell: (194.34, 183.28, 165.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 41 16.00 P 360 15.00 O 5558 8.00 N 4256 7.00 C 13508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 5.85 Conformation dependent library (CDL) restraints added in 2.5 seconds 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4244 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 17 sheets defined 70.8% alpha, 4.7% beta 114 base pairs and 166 stacking pairs defined. Time for finding SS restraints: 9.89 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 Processing helix chain 'A' and resid 15 through 16 No H-bonds generated for 'chain 'A' and resid 15 through 16' Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 26 through 34 removed outlier: 3.660A pdb=" N PHE A 31 " --> pdb=" O ALA A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 4.288A pdb=" N GLU A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 83 through 112 Processing helix chain 'A' and resid 119 through 131 removed outlier: 3.549A pdb=" N ARG A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 153 removed outlier: 3.873A pdb=" N VAL A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.706A pdb=" N ASP A 168 " --> pdb=" O ARG A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 178 No H-bonds generated for 'chain 'A' and resid 176 through 178' Processing helix chain 'A' and resid 179 through 185 removed outlier: 3.825A pdb=" N GLU A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 20 Processing helix chain 'B' and resid 26 through 37 removed outlier: 3.770A pdb=" N THR B 30 " --> pdb=" O GLY B 26 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B 37 " --> pdb=" O HIS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 83 through 114 removed outlier: 4.089A pdb=" N PHE B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU B 106 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 113 " --> pdb=" O ARG B 109 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 132 removed outlier: 3.524A pdb=" N LEU B 120 " --> pdb=" O ASP B 116 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA B 122 " --> pdb=" O GLY B 118 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ARG B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 153 Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'C' and resid 8 through 13 Processing helix chain 'C' and resid 13 through 20 removed outlier: 3.562A pdb=" N TYR C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 45 through 54 Processing helix chain 'C' and resid 60 through 69 removed outlier: 3.538A pdb=" N GLU C 64 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL C 68 " --> pdb=" O GLU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 112 Processing helix chain 'C' and resid 116 through 134 removed outlier: 3.517A pdb=" N GLN C 134 " --> pdb=" O GLU C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 153 Processing helix chain 'C' and resid 160 through 167 Processing helix chain 'C' and resid 179 through 189 Processing helix chain 'D' and resid 8 through 13 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 23 through 36 removed outlier: 3.566A pdb=" N MET D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 56 Processing helix chain 'D' and resid 61 through 66 Processing helix chain 'D' and resid 83 through 114 removed outlier: 3.574A pdb=" N TYR D 95 " --> pdb=" O GLU D 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY D 113 " --> pdb=" O ARG D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 132 Processing helix chain 'D' and resid 139 through 153 removed outlier: 3.898A pdb=" N VAL D 143 " --> pdb=" O SER D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 171 removed outlier: 4.044A pdb=" N TRP D 166 " --> pdb=" O GLY D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 178 No H-bonds generated for 'chain 'D' and resid 176 through 178' Processing helix chain 'D' and resid 179 through 189 removed outlier: 3.529A pdb=" N GLU D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 12 removed outlier: 3.653A pdb=" N THR E 12 " --> pdb=" O SER E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 20 removed outlier: 3.826A pdb=" N PHE E 20 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 39 removed outlier: 3.881A pdb=" N ARG E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 61 through 69 removed outlier: 4.515A pdb=" N MET E 67 " --> pdb=" O ALA E 63 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 78 removed outlier: 3.518A pdb=" N GLN E 78 " --> pdb=" O ARG E 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 75 through 78' Processing helix chain 'E' and resid 83 through 114 removed outlier: 3.610A pdb=" N TYR E 95 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY E 113 " --> pdb=" O ARG E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 133 removed outlier: 4.313A pdb=" N ALA E 122 " --> pdb=" O GLY E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 153 Processing helix chain 'E' and resid 160 through 169 removed outlier: 3.548A pdb=" N LYS E 169 " --> pdb=" O THR E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 188 Processing helix chain 'F' and resid 8 through 13 Processing helix chain 'F' and resid 13 through 19 Processing helix chain 'F' and resid 23 through 37 removed outlier: 3.665A pdb=" N GLU F 29 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN F 37 " --> pdb=" O HIS F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 61 through 68 removed outlier: 3.946A pdb=" N MET F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL F 68 " --> pdb=" O GLU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 114 removed outlier: 3.662A pdb=" N TYR F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY F 113 " --> pdb=" O ARG F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 133 Processing helix chain 'F' and resid 139 through 153 removed outlier: 3.506A pdb=" N VAL F 143 " --> pdb=" O SER F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 171 Processing helix chain 'F' and resid 179 through 189 Processing helix chain 'G' and resid 8 through 13 Processing helix chain 'G' and resid 15 through 21 Processing helix chain 'G' and resid 23 through 36 removed outlier: 3.684A pdb=" N ALA G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU G 29 " --> pdb=" O ARG G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 56 Processing helix chain 'G' and resid 60 through 69 removed outlier: 4.061A pdb=" N GLU G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 113 removed outlier: 3.630A pdb=" N TYR G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY G 113 " --> pdb=" O ARG G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 134 Processing helix chain 'G' and resid 139 through 153 removed outlier: 3.637A pdb=" N VAL G 143 " --> pdb=" O SER G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 171 removed outlier: 3.602A pdb=" N LYS G 169 " --> pdb=" O THR G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 189 Processing helix chain 'H' and resid 8 through 13 Processing helix chain 'H' and resid 13 through 20 Processing helix chain 'H' and resid 24 through 37 removed outlier: 4.102A pdb=" N MET H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN H 37 " --> pdb=" O HIS H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 56 Processing helix chain 'H' and resid 60 through 69 removed outlier: 4.145A pdb=" N GLU H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU H 66 " --> pdb=" O TRP H 62 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N MET H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL H 68 " --> pdb=" O GLU H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 114 removed outlier: 3.671A pdb=" N ARG H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY H 113 " --> pdb=" O ARG H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 134 removed outlier: 3.556A pdb=" N ALA H 122 " --> pdb=" O GLY H 118 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 153 Processing helix chain 'H' and resid 160 through 169 removed outlier: 3.548A pdb=" N LYS H 169 " --> pdb=" O THR H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 178 No H-bonds generated for 'chain 'H' and resid 176 through 178' Processing helix chain 'H' and resid 179 through 188 removed outlier: 3.682A pdb=" N VAL H 188 " --> pdb=" O LEU H 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 13 Processing helix chain 'I' and resid 15 through 20 Processing helix chain 'I' and resid 23 through 37 removed outlier: 3.689A pdb=" N ASN I 37 " --> pdb=" O HIS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 56 Processing helix chain 'I' and resid 60 through 68 removed outlier: 4.206A pdb=" N GLU I 64 " --> pdb=" O GLU I 60 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET I 67 " --> pdb=" O ALA I 63 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL I 68 " --> pdb=" O GLU I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 114 removed outlier: 3.539A pdb=" N TYR I 95 " --> pdb=" O GLU I 91 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY I 113 " --> pdb=" O ARG I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 133 Processing helix chain 'I' and resid 139 through 153 removed outlier: 3.513A pdb=" N VAL I 143 " --> pdb=" O SER I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 169 Processing helix chain 'I' and resid 176 through 178 No H-bonds generated for 'chain 'I' and resid 176 through 178' Processing helix chain 'I' and resid 179 through 188 removed outlier: 3.632A pdb=" N LEU I 187 " --> pdb=" O ILE I 183 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL I 188 " --> pdb=" O LEU I 184 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 13 Processing helix chain 'J' and resid 13 through 19 Processing helix chain 'J' and resid 24 through 37 removed outlier: 4.047A pdb=" N ASN J 37 " --> pdb=" O HIS J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 56 Processing helix chain 'J' and resid 60 through 68 removed outlier: 4.451A pdb=" N GLU J 64 " --> pdb=" O GLU J 60 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N MET J 67 " --> pdb=" O ALA J 63 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL J 68 " --> pdb=" O GLU J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 78 Processing helix chain 'J' and resid 83 through 113 removed outlier: 4.356A pdb=" N GLY J 113 " --> pdb=" O ARG J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 119 through 134 removed outlier: 3.869A pdb=" N GLN J 134 " --> pdb=" O GLU J 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 152 removed outlier: 3.604A pdb=" N VAL J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 169 removed outlier: 3.662A pdb=" N LYS J 169 " --> pdb=" O THR J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 176 through 178 No H-bonds generated for 'chain 'J' and resid 176 through 178' Processing helix chain 'J' and resid 179 through 189 removed outlier: 3.603A pdb=" N SER J 186 " --> pdb=" O ASN J 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 13 Processing helix chain 'K' and resid 13 through 20 removed outlier: 3.534A pdb=" N PHE K 20 " --> pdb=" O ILE K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 26 through 36 Processing helix chain 'K' and resid 45 through 55 Processing helix chain 'K' and resid 61 through 66 removed outlier: 3.657A pdb=" N GLU K 66 " --> pdb=" O TRP K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 111 Processing helix chain 'K' and resid 112 through 114 No H-bonds generated for 'chain 'K' and resid 112 through 114' Processing helix chain 'K' and resid 116 through 132 removed outlier: 3.575A pdb=" N LEU K 120 " --> pdb=" O ASP K 116 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA K 122 " --> pdb=" O GLY K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 153 Processing helix chain 'K' and resid 160 through 171 Processing helix chain 'K' and resid 179 through 187 Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 13 through 20 Processing helix chain 'L' and resid 27 through 36 removed outlier: 4.430A pdb=" N LEU L 34 " --> pdb=" O THR L 30 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU L 36 " --> pdb=" O ILE L 32 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 56 Processing helix chain 'L' and resid 62 through 66 Processing helix chain 'L' and resid 83 through 114 removed outlier: 3.811A pdb=" N PHE L 89 " --> pdb=" O PHE L 85 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG L 94 " --> pdb=" O ILE L 90 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR L 95 " --> pdb=" O GLU L 91 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY L 113 " --> pdb=" O ARG L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 116 through 134 removed outlier: 4.511A pdb=" N ALA L 122 " --> pdb=" O GLY L 118 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG L 123 " --> pdb=" O LYS L 119 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN L 134 " --> pdb=" O GLU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 153 removed outlier: 3.570A pdb=" N VAL L 145 " --> pdb=" O GLU L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 171 removed outlier: 3.510A pdb=" N LYS L 169 " --> pdb=" O THR L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 176 through 187 removed outlier: 4.544A pdb=" N LYS L 181 " --> pdb=" O PRO L 177 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASN L 182 " --> pdb=" O LYS L 178 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 82 Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.083A pdb=" N PHE B 4 " --> pdb=" O TYR B 43 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL B 5 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LYS B 173 " --> pdb=" O LEU B 156 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.548A pdb=" N ILE C 175 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'C' and resid 80 through 82 Processing sheet with id=AA6, first strand: chain 'D' and resid 69 through 71 removed outlier: 7.017A pdb=" N PHE D 42 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL D 3 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL D 157 " --> pdb=" O VAL D 3 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL D 5 " --> pdb=" O VAL D 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 70 through 71 removed outlier: 7.092A pdb=" N PHE E 42 " --> pdb=" O LYS E 70 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE E 4 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 80 through 82 Processing sheet with id=AA9, first strand: chain 'F' and resid 69 through 71 removed outlier: 6.984A pdb=" N PHE F 42 " --> pdb=" O LYS F 70 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL F 3 " --> pdb=" O VAL F 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 70 through 71 removed outlier: 7.289A pdb=" N PHE G 42 " --> pdb=" O LYS G 70 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL G 3 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N VAL G 157 " --> pdb=" O VAL G 3 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL G 5 " --> pdb=" O VAL G 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 80 through 82 Processing sheet with id=AB3, first strand: chain 'H' and resid 70 through 71 Processing sheet with id=AB4, first strand: chain 'I' and resid 69 through 71 removed outlier: 7.012A pdb=" N PHE I 42 " --> pdb=" O LYS I 70 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL I 3 " --> pdb=" O VAL I 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 80 through 82 Processing sheet with id=AB6, first strand: chain 'J' and resid 69 through 71 removed outlier: 6.654A pdb=" N PHE J 42 " --> pdb=" O LYS J 70 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL J 3 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL J 157 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL J 5 " --> pdb=" O VAL J 157 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AB8, first strand: chain 'K' and resid 80 through 82 1021 hydrogen bonds defined for protein. 3038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 314 hydrogen bonds 540 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 166 stacking parallelities Total time for adding SS restraints: 8.53 Time building geometry restraints manager: 6.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5103 1.33 - 1.45: 7133 1.45 - 1.57: 11823 1.57 - 1.69: 720 1.69 - 1.81: 82 Bond restraints: 24861 Sorted by residual: bond pdb=" N ASN A 13 " pdb=" CA ASN A 13 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.16e-02 7.43e+03 8.37e+00 bond pdb=" N ILE H 32 " pdb=" CA ILE H 32 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.14e-02 7.69e+03 7.34e+00 bond pdb=" N ILE J 97 " pdb=" CA ILE J 97 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.32e+00 bond pdb=" N ARG J 96 " pdb=" CA ARG J 96 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.17e-02 7.31e+03 7.17e+00 bond pdb=" N GLU J 91 " pdb=" CA GLU J 91 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.18e-02 7.18e+03 7.02e+00 ... (remaining 24856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 34971 2.02 - 4.04: 489 4.04 - 6.06: 46 6.06 - 8.08: 9 8.08 - 10.10: 1 Bond angle restraints: 35516 Sorted by residual: angle pdb=" N VAL A 10 " pdb=" CA VAL A 10 " pdb=" C VAL A 10 " ideal model delta sigma weight residual 113.71 107.69 6.02 9.50e-01 1.11e+00 4.01e+01 angle pdb=" C GLU F 22 " pdb=" CA GLU F 22 " pdb=" CB GLU F 22 " ideal model delta sigma weight residual 115.79 109.71 6.08 1.19e+00 7.06e-01 2.61e+01 angle pdb=" N GLY I 59 " pdb=" CA GLY I 59 " pdb=" C GLY I 59 " ideal model delta sigma weight residual 111.67 115.45 -3.78 9.20e-01 1.18e+00 1.69e+01 angle pdb=" C GLU H 21 " pdb=" CA GLU H 21 " pdb=" CB GLU H 21 " ideal model delta sigma weight residual 115.89 110.66 5.23 1.32e+00 5.74e-01 1.57e+01 angle pdb=" CA GLU C 185 " pdb=" CB GLU C 185 " pdb=" CG GLU C 185 " ideal model delta sigma weight residual 114.10 121.88 -7.78 2.00e+00 2.50e-01 1.51e+01 ... (remaining 35511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 13883 34.45 - 68.90: 1547 68.90 - 103.35: 203 103.35 - 137.79: 1 137.79 - 172.24: 2 Dihedral angle restraints: 15636 sinusoidal: 9125 harmonic: 6511 Sorted by residual: dihedral pdb=" C4' U T 60 " pdb=" C3' U T 60 " pdb=" C2' U T 60 " pdb=" C1' U T 60 " ideal model delta sinusoidal sigma weight residual -35.00 34.45 -69.45 1 8.00e+00 1.56e-02 9.73e+01 dihedral pdb=" C5' U T 60 " pdb=" C4' U T 60 " pdb=" C3' U T 60 " pdb=" O3' U T 60 " ideal model delta sinusoidal sigma weight residual 147.00 81.50 65.50 1 8.00e+00 1.56e-02 8.78e+01 dihedral pdb=" O4' U T 60 " pdb=" C4' U T 60 " pdb=" C3' U T 60 " pdb=" C2' U T 60 " ideal model delta sinusoidal sigma weight residual 24.00 -34.35 58.35 1 8.00e+00 1.56e-02 7.13e+01 ... (remaining 15633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3938 0.061 - 0.122: 415 0.122 - 0.183: 19 0.183 - 0.245: 5 0.245 - 0.306: 1 Chirality restraints: 4378 Sorted by residual: chirality pdb=" C3' U T 60 " pdb=" C4' U T 60 " pdb=" O3' U T 60 " pdb=" C2' U T 60 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C2' U T 60 " pdb=" C3' U T 60 " pdb=" O2' U T 60 " pdb=" C1' U T 60 " both_signs ideal model delta sigma weight residual False -2.52 -2.74 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE H 32 " pdb=" N ILE H 32 " pdb=" C ILE H 32 " pdb=" CB ILE H 32 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 4375 not shown) Planarity restraints: 3276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER J 73 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO J 74 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO J 74 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 74 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 73 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO D 74 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 74 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 74 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 81 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO G 82 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO G 82 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 82 " 0.032 5.00e-02 4.00e+02 ... (remaining 3273 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2649 2.74 - 3.28: 23269 3.28 - 3.82: 47266 3.82 - 4.36: 53530 4.36 - 4.90: 79791 Nonbonded interactions: 206505 Sorted by model distance: nonbonded pdb=" O6 G N 26 " pdb=" N1 A N 44 " model vdw 2.203 2.496 nonbonded pdb=" OH TYR G 49 " pdb=" OE2 GLU G 66 " model vdw 2.216 3.040 nonbonded pdb=" NH2 ARG H 109 " pdb=" O3' C T 56 " model vdw 2.228 3.120 nonbonded pdb=" O2' U T 16 " pdb=" OP2 G T 19 " model vdw 2.231 3.040 nonbonded pdb=" O2' G M 15 " pdb=" O6 G M 20 " model vdw 2.232 3.040 ... (remaining 206500 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 3 through 20 or resid 26 through 57 or resid 61 through 12 \ 8 or resid 130 through 187)) selection = (chain 'B' and (resid 3 through 16 or resid 18 through 20 or resid 26 through 57 \ or resid 61 through 128 or resid 130 through 187)) selection = (chain 'C' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'F' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'G' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'I' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'J' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'K' and (resid 3 through 16 or resid 18 through 20 or resid 26 through 57 \ or resid 61 through 128 or resid 130 through 187)) selection = (chain 'L' and (resid 3 through 16 or resid 18 through 128 or resid 130 through \ 187)) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'T' } 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=0.31 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: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.070 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 61.740 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24861 Z= 0.142 Angle : 0.579 10.097 35516 Z= 0.320 Chirality : 0.037 0.306 4378 Planarity : 0.004 0.060 3276 Dihedral : 23.781 172.242 11392 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 8.49 % Allowed : 34.61 % Favored : 56.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2191 helix: 0.62 (0.14), residues: 1369 sheet: -2.47 (0.43), residues: 99 loop : -1.77 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP J 166 HIS 0.020 0.003 HIS E 33 PHE 0.013 0.001 PHE J 65 TYR 0.021 0.002 TYR F 17 ARG 0.006 0.000 ARG E 133 Details of bonding type rmsd hydrogen bonds : bond 0.12967 ( 1335) hydrogen bonds : angle 5.44389 ( 3578) covalent geometry : bond 0.00267 (24861) covalent geometry : angle 0.57876 (35516) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 208 time to evaluate : 2.033 Fit side-chains revert: symmetry clash REVERT: C 185 GLU cc_start: 0.5322 (tm-30) cc_final: 0.4229 (mm-30) REVERT: D 11 PHE cc_start: 0.5930 (OUTLIER) cc_final: 0.5490 (p90) REVERT: E 119 LYS cc_start: 0.7564 (pttt) cc_final: 0.6995 (pptt) REVERT: F 51 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7392 (mm-30) REVERT: G 175 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6739 (tp) REVERT: I 151 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6940 (pt0) REVERT: J 54 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.6914 (mtmt) outliers start: 114 outliers final: 95 residues processed: 319 average time/residue: 1.1368 time to fit residues: 424.7139 Evaluate side-chains 291 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 192 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain D residue 125 ARG Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 64 GLU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 114 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 175 ILE Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain H residue 11 PHE Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 106 GLU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain I residue 2 ASP Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 117 VAL Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 54 LYS Chi-restraints excluded: chain J residue 61 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 178 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 20.0000 chunk 189 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 127 optimal weight: 1.9990 chunk 101 optimal weight: 0.0050 chunk 195 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN J 33 HIS J 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.227171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.195551 restraints weight = 40513.507| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 1.94 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4301 r_free = 0.4301 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4301 r_free = 0.4301 target_work(ls_wunit_k1) = 0.193 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24861 Z= 0.125 Angle : 0.540 9.496 35516 Z= 0.277 Chirality : 0.036 0.226 4378 Planarity : 0.005 0.063 3276 Dihedral : 22.835 163.585 8398 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 9.00 % Allowed : 31.29 % Favored : 59.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2191 helix: 0.88 (0.14), residues: 1412 sheet: -2.68 (0.39), residues: 99 loop : -1.85 (0.22), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 166 HIS 0.018 0.002 HIS E 33 PHE 0.016 0.002 PHE E 65 TYR 0.029 0.002 TYR J 17 ARG 0.004 0.000 ARG G 109 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 1335) hydrogen bonds : angle 4.07450 ( 3578) covalent geometry : bond 0.00271 (24861) covalent geometry : angle 0.53969 (35516) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 211 time to evaluate : 1.953 Fit side-chains revert: symmetry clash REVERT: D 11 PHE cc_start: 0.6053 (OUTLIER) cc_final: 0.5684 (p90) REVERT: D 78 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7320 (pt0) REVERT: D 176 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.6050 (p0) REVERT: E 41 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.5124 (tp30) REVERT: E 106 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: F 109 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.5262 (mpt-90) REVERT: G 102 ARG cc_start: 0.7844 (tpp-160) cc_final: 0.7609 (mpp-170) REVERT: H 91 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6801 (tt0) REVERT: I 15 GLU cc_start: 0.5535 (tp30) cc_final: 0.5332 (tp30) REVERT: I 60 GLU cc_start: 0.5577 (OUTLIER) cc_final: 0.5059 (mm-30) REVERT: I 121 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7347 (mp) outliers start: 121 outliers final: 60 residues processed: 309 average time/residue: 1.2076 time to fit residues: 432.2587 Evaluate side-chains 264 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 195 time to evaluate : 2.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 178 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 203 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 228 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 159 optimal weight: 0.0980 chunk 96 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 4 optimal weight: 20.0000 chunk 223 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN D 179 ASN E 24 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN J 33 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.226701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.192488 restraints weight = 35363.403| |-----------------------------------------------------------------------------| r_work (start): 0.4271 rms_B_bonded: 1.97 r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4271 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4271 r_free = 0.4271 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4271 r_free = 0.4271 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4271 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24861 Z= 0.127 Angle : 0.533 9.893 35516 Z= 0.273 Chirality : 0.036 0.208 4378 Planarity : 0.005 0.059 3276 Dihedral : 22.539 162.558 8311 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 9.82 % Allowed : 30.26 % Favored : 59.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.18), residues: 2191 helix: 1.05 (0.14), residues: 1420 sheet: -2.81 (0.37), residues: 99 loop : -1.81 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 166 HIS 0.015 0.002 HIS E 33 PHE 0.013 0.002 PHE E 65 TYR 0.025 0.002 TYR J 17 ARG 0.003 0.000 ARG H 109 Details of bonding type rmsd hydrogen bonds : bond 0.04207 ( 1335) hydrogen bonds : angle 3.86772 ( 3578) covalent geometry : bond 0.00283 (24861) covalent geometry : angle 0.53257 (35516) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 212 time to evaluate : 1.920 Fit side-chains REVERT: C 117 VAL cc_start: 0.7544 (OUTLIER) cc_final: 0.7307 (p) REVERT: C 130 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6729 (tt0) REVERT: D 11 PHE cc_start: 0.6002 (OUTLIER) cc_final: 0.5323 (p90) REVERT: D 38 SER cc_start: 0.6423 (t) cc_final: 0.6106 (m) REVERT: D 55 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7089 (mp) REVERT: D 78 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7329 (pt0) REVERT: E 41 GLU cc_start: 0.5890 (OUTLIER) cc_final: 0.5224 (tp30) REVERT: E 55 ILE cc_start: 0.6419 (mt) cc_final: 0.6185 (mp) REVERT: E 106 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6508 (mp0) REVERT: F 109 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.5063 (mtt-85) REVERT: F 130 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6483 (tt0) REVERT: H 91 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.7020 (tt0) REVERT: I 121 ILE cc_start: 0.7687 (OUTLIER) cc_final: 0.7297 (mp) REVERT: I 176 ASP cc_start: 0.6897 (OUTLIER) cc_final: 0.6474 (p0) outliers start: 132 outliers final: 52 residues processed: 312 average time/residue: 1.1954 time to fit residues: 435.1101 Evaluate side-chains 263 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 199 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 178 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 177 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 191 optimal weight: 50.0000 chunk 130 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 105 optimal weight: 5.9990 chunk 239 optimal weight: 40.0000 chunk 210 optimal weight: 30.0000 chunk 156 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 179 ASN E 24 GLN F 179 ASN J 33 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.228514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.193328 restraints weight = 33531.924| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 1.93 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4281 r_free = 0.4281 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4281 r_free = 0.4281 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 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 : 0.002 0.047 24861 Z= 0.113 Angle : 0.512 10.168 35516 Z= 0.261 Chirality : 0.035 0.198 4378 Planarity : 0.004 0.062 3276 Dihedral : 22.340 162.517 8283 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 8.27 % Allowed : 32.55 % Favored : 59.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.18), residues: 2191 helix: 1.23 (0.14), residues: 1422 sheet: -2.66 (0.39), residues: 99 loop : -1.78 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP E 166 HIS 0.012 0.002 HIS E 33 PHE 0.016 0.001 PHE J 31 TYR 0.024 0.002 TYR J 17 ARG 0.003 0.000 ARG F 25 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 1335) hydrogen bonds : angle 3.76866 ( 3578) covalent geometry : bond 0.00250 (24861) covalent geometry : angle 0.51193 (35516) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4382 Ramachandran restraints generated. 2191 Oldfield, 0 Emsley, 2191 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 218 time to evaluate : 1.913 Fit side-chains REVERT: C 117 VAL cc_start: 0.7524 (t) cc_final: 0.7258 (p) REVERT: C 130 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6727 (tt0) REVERT: D 11 PHE cc_start: 0.6065 (OUTLIER) cc_final: 0.5219 (p90) REVERT: D 78 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7306 (pt0) REVERT: D 141 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6802 (pt0) REVERT: E 41 GLU cc_start: 0.5800 (OUTLIER) cc_final: 0.5094 (tp30) REVERT: E 55 ILE cc_start: 0.6357 (mt) cc_final: 0.6096 (mp) REVERT: E 106 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6339 (mp0) REVERT: F 130 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.6407 (tt0) REVERT: I 121 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7244 (mp) REVERT: I 140 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.6440 (pptt) outliers start: 111 outliers final: 43 residues processed: 305 average time/residue: 1.3418 time to fit residues: 476.0780 Evaluate side-chains 247 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 195 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 140 LYS Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 178 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.5394 > 50: distance: 102 - 108: 5.621 distance: 103 - 132: 16.115 distance: 108 - 109: 6.613 distance: 109 - 110: 5.649 distance: 109 - 112: 8.484 distance: 110 - 111: 5.462 distance: 110 - 117: 10.190 distance: 111 - 140: 14.608 distance: 112 - 113: 12.450 distance: 113 - 114: 3.911 distance: 114 - 115: 8.096 distance: 114 - 116: 13.203 distance: 117 - 118: 7.002 distance: 118 - 119: 13.060 distance: 118 - 121: 13.696 distance: 119 - 120: 23.343 distance: 119 - 125: 27.676 distance: 120 - 147: 19.331 distance: 121 - 122: 9.718 distance: 122 - 123: 9.076 distance: 122 - 124: 10.655 distance: 125 - 126: 26.326 distance: 126 - 127: 9.802 distance: 126 - 129: 10.291 distance: 127 - 128: 15.859 distance: 127 - 132: 9.553 distance: 128 - 155: 13.144 distance: 129 - 130: 42.128 distance: 129 - 131: 46.278 distance: 132 - 133: 7.219 distance: 133 - 134: 11.429 distance: 133 - 136: 11.256 distance: 134 - 135: 9.336 distance: 134 - 140: 8.660 distance: 135 - 163: 7.838 distance: 136 - 137: 9.337 distance: 137 - 138: 7.152 distance: 137 - 139: 3.782 distance: 140 - 141: 12.423 distance: 141 - 142: 5.957 distance: 141 - 144: 8.221 distance: 142 - 143: 10.961 distance: 142 - 147: 8.554 distance: 143 - 171: 10.196 distance: 144 - 145: 13.443 distance: 144 - 146: 10.209 distance: 147 - 148: 3.075 distance: 148 - 149: 3.231 distance: 148 - 151: 6.154 distance: 149 - 150: 9.118 distance: 149 - 155: 4.917 distance: 150 - 176: 12.359 distance: 151 - 152: 14.331 distance: 152 - 153: 7.649 distance: 152 - 154: 10.712 distance: 155 - 156: 3.492 distance: 156 - 157: 4.893 distance: 156 - 159: 4.150 distance: 157 - 158: 8.477 distance: 157 - 163: 6.853 distance: 158 - 188: 9.073 distance: 159 - 160: 4.892 distance: 160 - 161: 14.071 distance: 160 - 162: 3.964 distance: 163 - 164: 6.063 distance: 165 - 171: 4.259 distance: 166 - 196: 7.224 distance: 167 - 168: 12.029 distance: 168 - 169: 7.399 distance: 168 - 170: 11.409 distance: 171 - 172: 3.600 distance: 172 - 173: 5.553 distance: 172 - 175: 8.304 distance: 173 - 174: 9.984 distance: 173 - 176: 10.975 distance: 174 - 204: 9.284 distance: 176 - 177: 5.057 distance: 177 - 178: 6.081 distance: 177 - 180: 3.827 distance: 178 - 179: 8.793 distance: 180 - 181: 4.480 distance: 181 - 183: 4.329 distance: 182 - 184: 3.134 distance: 184 - 186: 4.742 distance: 185 - 186: 4.124 distance: 186 - 187: 6.430