Starting phenix.real_space_refine on Fri Aug 7 17:08:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd9_37128/08_2026/8kd9_37128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd9_37128/08_2026/8kd9_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_37128/08_2026/8kd9_37128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd9_37128/08_2026/8kd9_37128.map" model { file = "/net/cci-nas-00/data/ceres_data/8kd9_37128/08_2026/8kd9_37128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd9_37128/08_2026/8kd9_37128.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: {'ASP:plan': 12, 'PHE:plan': 10, 'ASN:plan1': 5, 'GLU:plan': 20, 'ARG:plan': 16, 'HIS:plan': 2, 'TYR:plan': 6, 'TRP:plan': 2, 'GLN:plan1': 2} 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: {'ASP:plan': 12, 'PHE:plan': 10, 'ASN:plan1': 5, 'GLU:plan': 22, 'TYR:plan': 7, 'ARG:plan': 16, 'HIS:plan': 2, 'TRP:plan': 2, 'GLN:plan1': 2} 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: {'PHE:plan': 10, 'ASP:plan': 11, 'ASN:plan1': 5, 'GLU:plan': 20, 'TYR:plan': 7, 'ARG:plan': 16, 'HIS:plan': 2, 'TRP:plan': 2, 'GLN:plan1': 2} 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: {'ASP:plan': 12, 'PHE:plan': 10, 'ASN:plan1': 5, 'GLU:plan': 19, 'TYR:plan': 7, 'ARG:plan': 15, 'HIS:plan': 2, 'TRP:plan': 2, 'GLN:plan1': 2} 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:plan': 1, ' A%5*END:plan2': 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:plan': 1, ' A%5*END:plan2': 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:plan': 1, ' A%5*END:plan2': 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:plan': 1, ' A%5*END:plan2': 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:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 6.19, per 1000 atoms: 0.26 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: 1.99 Conformation dependent library (CDL) restraints added in 1.1 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: 3.36 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: 3.99 Time building geometry restraints manager: 2.59 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: 34159 2.02 - 4.04: 1301 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=" C1' C M 66 " pdb=" N1 C M 66 " pdb=" C2 C M 66 " ideal model delta sigma weight residual 118.80 123.40 -4.60 1.10e+00 8.26e-01 1.75e+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=" C1' C T 6 " pdb=" N1 C T 6 " pdb=" C2 C T 6 " ideal model delta sigma weight residual 118.80 123.29 -4.49 1.10e+00 8.26e-01 1.66e+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: 3558 0.061 - 0.122: 491 0.122 - 0.183: 323 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=" C1' G M 52 " pdb=" O4' G M 52 " pdb=" C2' G M 52 " pdb=" N9 G M 52 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" C1' G T 52 " pdb=" O4' G T 52 " pdb=" C2' G T 52 " pdb=" N9 G T 52 " both_signs ideal model delta sigma weight residual False 2.47 2.26 0.21 2.00e-01 2.50e+01 1.12e+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: 5.250 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: 0.820 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.550 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 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:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 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= 0.182 Angle : 0.699 10.097 35516 Z= 0.538 Chirality : 0.052 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (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 ARG 0.006 0.000 ARG E 133 TYR 0.021 0.002 TYR F 17 PHE 0.013 0.001 PHE J 65 TRP 0.026 0.003 TRP J 166 HIS 0.020 0.003 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.18 (24861) covalent geometry : angle 0.69934 / 0.54 (35516) hydrogen bonds : bond 0.12967 / 9.80 ( 1335) hydrogen bonds : angle 5.44389 / 4.15 ( 3578) *********************** 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 : 0.787 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: 0.6915 (mtmt) outliers start: 114 outliers final: 95 residues processed: 319 average time/residue: 0.4988 time to fit residues: 187.7740 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 : 0.462 ------------------------------------------------------------------------------- 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 216 optimal weight: 50.0000 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.7980 chunk 247 optimal weight: 50.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 179 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4623 r_free = 0.4623 target = 0.226886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.193065 restraints weight = 34729.861| |-----------------------------------------------------------------------------| r_work (start): 0.4282 rms_B_bonded: 1.92 r_work (final): 0.4282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4282 r_free = 0.4282 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4282 r_free = 0.4282 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.4282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24861 Z= 0.127 Angle : 0.513 10.779 35516 Z= 0.290 Chirality : 0.037 0.195 4378 Planarity : 0.005 0.063 3276 Dihedral : 23.069 167.523 8398 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 9.82 % Allowed : 31.51 % Favored : 58.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.18), residues: 2191 helix: 0.83 (0.14), residues: 1409 sheet: -2.70 (0.39), residues: 99 loop : -1.89 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 109 TYR 0.027 0.002 TYR J 17 PHE 0.015 0.002 PHE G 180 TRP 0.019 0.003 TRP E 166 HIS 0.017 0.002 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (24861) covalent geometry : angle 0.51293 / 0.29 (35516) hydrogen bonds : bond 0.05384 / 4.07 ( 1335) hydrogen bonds : angle 4.31471 / 3.28 ( 3578) *********************** 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 336 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 204 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 123 ARG cc_start: 0.6353 (ttp-110) cc_final: 0.6097 (ttp80) REVERT: D 11 PHE cc_start: 0.5909 (OUTLIER) cc_final: 0.5592 (p90) REVERT: E 60 GLU cc_start: 0.5621 (tp30) cc_final: 0.5410 (mm-30) REVERT: H 70 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7394 (mttm) REVERT: I 15 GLU cc_start: 0.5541 (tp30) cc_final: 0.5337 (tp30) REVERT: I 121 ILE cc_start: 0.7627 (OUTLIER) cc_final: 0.7281 (mp) REVERT: J 92 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6790 (tt0) outliers start: 132 outliers final: 83 residues processed: 314 average time/residue: 0.5055 time to fit residues: 186.7803 Evaluate side-chains 276 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 189 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 91 GLU 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 50 THR Chi-restraints excluded: chain D residue 68 VAL 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 156 LEU Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 THR 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 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 68 VAL Chi-restraints excluded: chain F residue 73 SER 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 9 SER Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 67 MET 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 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 91 GLU Chi-restraints excluded: chain H residue 106 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 80 THR 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 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 61 LEU Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 92 GLU Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 175 ILE 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 94 optimal weight: 0.9990 chunk 235 optimal weight: 20.0000 chunk 101 optimal weight: 0.4980 chunk 132 optimal weight: 5.9990 chunk 147 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 198 optimal weight: 30.0000 chunk 35 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 131 optimal weight: 7.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.227253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.193484 restraints weight = 39047.938| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 2.06 r_work (final): 0.4283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4282 r_free = 0.4282 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4282 r_free = 0.4282 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.0931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24861 Z= 0.117 Angle : 0.482 10.321 35516 Z= 0.272 Chirality : 0.036 0.241 4378 Planarity : 0.005 0.063 3276 Dihedral : 22.824 166.624 8344 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 10.48 % Allowed : 30.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.18), residues: 2191 helix: 1.03 (0.14), residues: 1406 sheet: -2.87 (0.37), residues: 99 loop : -1.84 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 109 TYR 0.025 0.002 TYR J 17 PHE 0.015 0.001 PHE G 180 TRP 0.018 0.003 TRP E 166 HIS 0.016 0.002 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (24861) covalent geometry : angle 0.48215 / 0.27 (35516) hydrogen bonds : bond 0.04856 / 3.68 ( 1335) hydrogen bonds : angle 4.04358 / 3.07 ( 3578) *********************** 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 343 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 202 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: C 117 VAL cc_start: 0.7640 (OUTLIER) cc_final: 0.7361 (p) REVERT: C 123 ARG cc_start: 0.6348 (ttp-110) cc_final: 0.6127 (ttp80) REVERT: D 11 PHE cc_start: 0.5908 (OUTLIER) cc_final: 0.5466 (p90) REVERT: D 51 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.5729 (mp0) REVERT: E 41 GLU cc_start: 0.5833 (OUTLIER) cc_final: 0.5146 (tp30) REVERT: F 109 ARG cc_start: 0.7260 (OUTLIER) cc_final: 0.5350 (mtt180) REVERT: F 146 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8527 (mt) REVERT: I 15 GLU cc_start: 0.5507 (tp30) cc_final: 0.5290 (tp30) REVERT: I 60 GLU cc_start: 0.5531 (OUTLIER) cc_final: 0.5056 (mm-30) REVERT: I 121 ILE cc_start: 0.7684 (OUTLIER) cc_final: 0.7346 (mp) REVERT: J 183 ILE cc_start: 0.5149 (OUTLIER) cc_final: 0.4866 (mt) outliers start: 141 outliers final: 81 residues processed: 322 average time/residue: 0.5554 time to fit residues: 209.3713 Evaluate side-chains 277 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 187 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 73 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 91 GLU 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 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 17 TYR Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 68 VAL 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 132 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR 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 121 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 157 VAL 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 73 SER Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 146 LEU 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 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 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 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 19 THR Chi-restraints excluded: chain I residue 60 GLU 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 121 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 146 LEU 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 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 178 LYS Chi-restraints excluded: chain J residue 183 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 113 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 249 optimal weight: 30.0000 chunk 52 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 216 optimal weight: 50.0000 chunk 111 optimal weight: 1.9990 chunk 195 optimal weight: 20.0000 chunk 208 optimal weight: 40.0000 chunk 182 optimal weight: 50.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 24 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.222332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.185508 restraints weight = 32485.127| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 1.89 r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4197 r_free = 0.4197 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4197 r_free = 0.4197 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 24861 Z= 0.235 Angle : 0.613 10.965 35516 Z= 0.332 Chirality : 0.041 0.201 4378 Planarity : 0.006 0.067 3276 Dihedral : 22.838 165.675 8322 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 11.22 % Allowed : 30.55 % Favored : 58.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.18), residues: 2191 helix: 0.71 (0.14), residues: 1395 sheet: -2.89 (0.38), residues: 83 loop : -1.96 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 123 TYR 0.025 0.002 TYR F 17 PHE 0.023 0.003 PHE G 180 TRP 0.020 0.004 TRP H 166 HIS 0.018 0.002 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.23 (24861) covalent geometry : angle 0.61289 / 0.33 (35516) hydrogen bonds : bond 0.05785 / 4.37 ( 1335) hydrogen bonds : angle 4.22197 / 3.20 ( 3578) *********************** 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 352 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 201 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: C 123 ARG cc_start: 0.6397 (OUTLIER) cc_final: 0.6161 (ttp80) REVERT: D 11 PHE cc_start: 0.6246 (OUTLIER) cc_final: 0.5870 (p90) REVERT: D 51 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.5809 (mp0) REVERT: D 78 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7328 (pt0) REVERT: E 106 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6297 (mp0) REVERT: F 109 ARG cc_start: 0.7382 (OUTLIER) cc_final: 0.5473 (mtt180) REVERT: G 102 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.6847 (mpp-170) REVERT: I 60 GLU cc_start: 0.5627 (OUTLIER) cc_final: 0.5110 (mm-30) REVERT: I 121 ILE cc_start: 0.7805 (OUTLIER) cc_final: 0.7481 (mp) REVERT: J 92 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6794 (tt0) outliers start: 151 outliers final: 84 residues processed: 329 average time/residue: 0.5699 time to fit residues: 219.4323 Evaluate side-chains 284 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 190 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 73 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 ARG 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 17 TYR Chi-restraints excluded: chain D residue 51 GLU 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 108 THR 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 187 LEU Chi-restraints excluded: chain E residue 8 THR 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 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 157 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain E residue 179 ASN 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 80 THR 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 54 LYS Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 112 SER 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 175 ILE Chi-restraints excluded: chain G residue 186 SER Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 37 ASN 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 112 SER 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 19 THR Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 80 THR 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 170 ILE Chi-restraints excluded: chain J residue 8 THR 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 92 GLU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 178 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 55 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 225 optimal weight: 50.0000 chunk 147 optimal weight: 0.9980 chunk 1 optimal weight: 10.0000 chunk 195 optimal weight: 30.0000 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 193 optimal weight: 5.9990 chunk 240 optimal weight: 50.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN E 24 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN J 33 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.223960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.189496 restraints weight = 34735.405| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.94 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4241 r_free = 0.4241 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4241 r_free = 0.4241 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24861 Z= 0.161 Angle : 0.533 10.728 35516 Z= 0.295 Chirality : 0.038 0.391 4378 Planarity : 0.005 0.062 3276 Dihedral : 22.770 164.950 8316 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 10.85 % Allowed : 30.63 % Favored : 58.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.18), residues: 2191 helix: 0.81 (0.14), residues: 1409 sheet: -2.96 (0.38), residues: 83 loop : -2.01 (0.21), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 123 TYR 0.025 0.002 TYR F 17 PHE 0.020 0.002 PHE G 180 TRP 0.023 0.004 TRP E 166 HIS 0.015 0.002 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (24861) covalent geometry : angle 0.53295 / 0.30 (35516) hydrogen bonds : bond 0.05157 / 3.90 ( 1335) hydrogen bonds : angle 4.13507 / 3.14 ( 3578) *********************** REFINEMENT MACRO_CYCLE 5 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 341 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 195 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: C 123 ARG cc_start: 0.6355 (OUTLIER) cc_final: 0.6126 (ttp80) REVERT: D 11 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5283 (p90) REVERT: D 28 MET cc_start: 0.5324 (tpt) cc_final: 0.5007 (tpt) REVERT: D 29 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.5546 (tm-30) REVERT: D 51 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.5645 (mp0) REVERT: D 54 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.7014 (ttpt) REVERT: D 78 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7350 (pt0) REVERT: E 41 GLU cc_start: 0.5992 (OUTLIER) cc_final: 0.5287 (tp30) REVERT: E 106 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: F 109 ARG cc_start: 0.7331 (OUTLIER) cc_final: 0.5431 (mtt180) REVERT: G 11 PHE cc_start: 0.6461 (OUTLIER) cc_final: 0.5609 (m-80) REVERT: G 102 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.6489 (mpp-170) REVERT: I 25 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6087 (ttt-90) REVERT: I 60 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.5124 (mm-30) REVERT: I 121 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7450 (mp) REVERT: J 92 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6810 (tt0) outliers start: 146 outliers final: 83 residues processed: 320 average time/residue: 0.5795 time to fit residues: 216.4873 Evaluate side-chains 285 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 187 time to evaluate : 0.751 ------------------------------------------------------------------------------- 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 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 117 VAL Chi-restraints excluded: chain C residue 123 ARG 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 17 TYR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 54 LYS 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 99 LYS Chi-restraints excluded: chain D residue 108 THR 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 187 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR 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 157 VAL Chi-restraints excluded: chain E residue 170 ILE 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 68 VAL Chi-restraints excluded: chain F residue 80 THR 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 11 PHE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 112 SER 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 12 THR Chi-restraints excluded: chain H residue 37 ASN 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 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 19 THR Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 60 GLU 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 121 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 170 ILE 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 92 GLU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 178 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 105 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 129 optimal weight: 0.3980 chunk 95 optimal weight: 2.9990 chunk 190 optimal weight: 40.0000 chunk 74 optimal weight: 0.7980 chunk 11 optimal weight: 50.0000 chunk 46 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 212 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 24 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.224382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.190577 restraints weight = 30942.741| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 1.67 r_work: 0.3923 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3914 r_free = 0.3914 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24861 Z= 0.151 Angle : 0.525 11.175 35516 Z= 0.291 Chirality : 0.037 0.229 4378 Planarity : 0.005 0.066 3276 Dihedral : 22.692 165.074 8313 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 10.63 % Allowed : 31.59 % Favored : 57.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.18), residues: 2191 helix: 0.87 (0.14), residues: 1414 sheet: -2.94 (0.39), residues: 83 loop : -1.98 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 123 TYR 0.025 0.002 TYR F 17 PHE 0.019 0.002 PHE G 180 TRP 0.022 0.003 TRP E 166 HIS 0.012 0.002 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (24861) covalent geometry : angle 0.52506 / 0.29 (35516) hydrogen bonds : bond 0.04990 / 3.77 ( 1335) hydrogen bonds : angle 4.05912 / 3.08 ( 3578) *********************** REFINEMENT MACRO_CYCLE 6 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 336 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 193 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: C 49 TYR cc_start: 0.7375 (t80) cc_final: 0.7142 (t80) REVERT: C 123 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6459 (ttp80) REVERT: D 11 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5170 (p90) REVERT: D 28 MET cc_start: 0.5561 (tpt) cc_final: 0.5226 (tpt) REVERT: D 29 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5646 (tm-30) REVERT: D 51 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.5873 (mp0) REVERT: D 78 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7397 (pt0) REVERT: E 41 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5805 (tp30) REVERT: E 106 GLU cc_start: 0.7272 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: F 51 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7685 (mm-30) REVERT: F 109 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.5679 (mtt180) REVERT: G 11 PHE cc_start: 0.6438 (OUTLIER) cc_final: 0.5634 (m-80) REVERT: G 102 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6608 (mpp-170) REVERT: I 25 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6402 (ttt-90) REVERT: I 60 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5630 (mm-30) REVERT: I 121 ILE cc_start: 0.7888 (OUTLIER) cc_final: 0.7593 (mp) REVERT: I 140 LYS cc_start: 0.7901 (OUTLIER) cc_final: 0.6541 (pptt) REVERT: J 92 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7280 (tt0) outliers start: 143 outliers final: 80 residues processed: 315 average time/residue: 0.5599 time to fit residues: 206.1962 Evaluate side-chains 282 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 187 time to evaluate : 0.648 ------------------------------------------------------------------------------- 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 81 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 ARG 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 17 TYR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 54 LYS 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 99 LYS Chi-restraints excluded: chain D residue 108 THR 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 187 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR 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 157 VAL Chi-restraints excluded: chain E residue 170 ILE 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 68 VAL Chi-restraints excluded: chain F residue 80 THR 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 11 PHE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 112 SER 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 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 117 VAL Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 186 SER 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 25 ARG Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 81 VAL 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 140 LYS Chi-restraints excluded: chain I residue 146 LEU 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 92 GLU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 178 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 50.0000 chunk 106 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 18 optimal weight: 30.0000 chunk 55 optimal weight: 0.6980 chunk 211 optimal weight: 7.9990 chunk 212 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 59 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 24 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.224781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.188629 restraints weight = 33020.090| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 1.88 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4231 r_free = 0.4231 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4231 r_free = 0.4231 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24861 Z= 0.146 Angle : 0.521 12.162 35516 Z= 0.288 Chirality : 0.037 0.260 4378 Planarity : 0.005 0.060 3276 Dihedral : 22.632 165.032 8307 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 9.67 % Allowed : 33.21 % Favored : 57.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 2191 helix: 0.93 (0.14), residues: 1414 sheet: -2.92 (0.39), residues: 83 loop : -1.92 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 123 TYR 0.024 0.002 TYR F 17 PHE 0.019 0.002 PHE G 180 TRP 0.022 0.003 TRP E 166 HIS 0.011 0.002 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (24861) covalent geometry : angle 0.52099 / 0.29 (35516) hydrogen bonds : bond 0.04866 / 3.68 ( 1335) hydrogen bonds : angle 4.01855 / 3.05 ( 3578) *********************** REFINEMENT MACRO_CYCLE 7 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: 130 poor density : 192 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: C 117 VAL cc_start: 0.7693 (OUTLIER) cc_final: 0.7402 (p) REVERT: C 123 ARG cc_start: 0.6374 (OUTLIER) cc_final: 0.6155 (ttp80) REVERT: D 11 PHE cc_start: 0.6008 (OUTLIER) cc_final: 0.5428 (p90) REVERT: D 29 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5488 (tm-30) REVERT: D 51 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.5852 (mp0) REVERT: D 54 LYS cc_start: 0.7213 (OUTLIER) cc_final: 0.6969 (ttpt) REVERT: D 78 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: E 41 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.5201 (tp30) REVERT: E 106 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: F 109 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.5410 (mtt180) REVERT: G 11 PHE cc_start: 0.6450 (OUTLIER) cc_final: 0.5678 (m-80) REVERT: G 102 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.6643 (mpp-170) REVERT: I 25 ARG cc_start: 0.6559 (OUTLIER) cc_final: 0.6279 (ttt-90) REVERT: I 60 GLU cc_start: 0.5681 (OUTLIER) cc_final: 0.5298 (mm-30) REVERT: I 121 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7491 (mp) REVERT: I 140 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.6477 (pptt) REVERT: J 92 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6873 (tt0) outliers start: 130 outliers final: 73 residues processed: 304 average time/residue: 0.5664 time to fit residues: 200.7740 Evaluate side-chains 287 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 197 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 81 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 123 ARG 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 17 TYR Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 51 GLU Chi-restraints excluded: chain D residue 54 LYS 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 99 LYS Chi-restraints excluded: chain D residue 108 THR 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 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 46 THR 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 157 VAL Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 80 THR 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 11 PHE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 112 SER 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 186 SER 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 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 19 THR Chi-restraints excluded: chain I residue 25 ARG Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 81 VAL 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 140 LYS Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 170 ILE 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 92 GLU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 146 LEU Chi-restraints excluded: chain J residue 178 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 140 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 209 optimal weight: 30.0000 chunk 106 optimal weight: 0.5980 chunk 243 optimal weight: 50.0000 chunk 52 optimal weight: 0.7980 chunk 2 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 24 GLN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.226776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.191457 restraints weight = 35109.722| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 2.03 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4263 r_free = 0.4263 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4263 r_free = 0.4263 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24861 Z= 0.117 Angle : 0.488 10.607 35516 Z= 0.273 Chirality : 0.036 0.157 4378 Planarity : 0.005 0.061 3276 Dihedral : 22.507 165.082 8292 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 8.12 % Allowed : 34.69 % Favored : 57.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.18), residues: 2191 helix: 1.11 (0.14), residues: 1410 sheet: -2.87 (0.35), residues: 111 loop : -1.81 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 123 TYR 0.024 0.002 TYR F 17 PHE 0.017 0.001 PHE G 180 TRP 0.023 0.003 TRP E 166 HIS 0.014 0.002 HIS J 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (24861) covalent geometry : angle 0.48844 / 0.27 (35516) hydrogen bonds : bond 0.04503 / 3.41 ( 1335) hydrogen bonds : angle 3.90493 / 2.96 ( 3578) *********************** REFINEMENT MACRO_CYCLE 8 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 310 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 201 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 123 ARG cc_start: 0.6396 (OUTLIER) cc_final: 0.6181 (ttp80) REVERT: D 11 PHE cc_start: 0.5726 (OUTLIER) cc_final: 0.5278 (p90) REVERT: D 51 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.5636 (mp0) REVERT: D 52 MET cc_start: 0.6444 (ttp) cc_final: 0.6118 (ttt) REVERT: D 78 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.7297 (pt0) REVERT: E 41 GLU cc_start: 0.5901 (OUTLIER) cc_final: 0.5204 (tp30) REVERT: E 55 ILE cc_start: 0.6579 (mt) cc_final: 0.6316 (mp) REVERT: E 106 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6510 (mp0) REVERT: E 175 ILE cc_start: 0.6781 (OUTLIER) cc_final: 0.6457 (tp) REVERT: F 109 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.5413 (mtt180) REVERT: G 11 PHE cc_start: 0.6428 (OUTLIER) cc_final: 0.5671 (m-80) REVERT: G 102 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6395 (mpp-170) REVERT: G 178 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5935 (mttt) REVERT: H 91 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6967 (tt0) REVERT: H 92 GLU cc_start: 0.7596 (tp30) cc_final: 0.7325 (tp30) REVERT: I 121 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7321 (mp) REVERT: I 140 LYS cc_start: 0.7614 (OUTLIER) cc_final: 0.6417 (pptt) outliers start: 109 outliers final: 63 residues processed: 291 average time/residue: 0.5582 time to fit residues: 189.0627 Evaluate side-chains 267 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 190 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 123 ARG 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 11 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 51 GLU 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 99 LYS Chi-restraints excluded: chain D residue 108 THR 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 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 64 GLU 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 157 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain F residue 10 VAL 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 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 11 PHE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 112 SER 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 178 LYS 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 51 GLU 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 117 VAL Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 186 SER Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 9 SER 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 146 LEU Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 175 ILE Chi-restraints excluded: chain J residue 178 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 163 optimal weight: 4.9990 chunk 205 optimal weight: 0.0770 chunk 197 optimal weight: 10.0000 chunk 192 optimal weight: 20.0000 chunk 135 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 246 optimal weight: 50.0000 chunk 165 optimal weight: 0.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.225676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.194030 restraints weight = 34677.260| |-----------------------------------------------------------------------------| r_work (start): 0.4291 rms_B_bonded: 1.79 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4291 r_free = 0.4291 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4291 r_free = 0.4291 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 24861 Z= 0.139 Angle : 0.511 13.149 35516 Z= 0.282 Chirality : 0.037 0.172 4378 Planarity : 0.005 0.059 3276 Dihedral : 22.457 165.200 8284 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 7.53 % Allowed : 35.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 2191 helix: 1.10 (0.14), residues: 1411 sheet: -2.78 (0.37), residues: 95 loop : -1.80 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 123 TYR 0.024 0.002 TYR F 17 PHE 0.019 0.002 PHE G 180 TRP 0.018 0.003 TRP E 166 HIS 0.010 0.002 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (24861) covalent geometry : angle 0.51141 / 0.28 (35516) hydrogen bonds : bond 0.04683 / 3.54 ( 1335) hydrogen bonds : angle 3.93046 / 2.98 ( 3578) *********************** REFINEMENT MACRO_CYCLE 9 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 293 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 192 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: C 17 TYR cc_start: 0.5031 (p90) cc_final: 0.4730 (p90) REVERT: C 123 ARG cc_start: 0.6362 (OUTLIER) cc_final: 0.6130 (ttp80) REVERT: C 130 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6690 (tt0) REVERT: D 11 PHE cc_start: 0.5804 (OUTLIER) cc_final: 0.5155 (p90) REVERT: D 51 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.5823 (mp0) REVERT: D 78 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7311 (pt0) REVERT: E 41 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.5281 (tp30) REVERT: E 55 ILE cc_start: 0.6600 (mt) cc_final: 0.6304 (mp) REVERT: E 106 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6520 (mp0) REVERT: E 175 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6511 (tp) REVERT: F 109 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.5395 (mtt180) REVERT: G 11 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.5773 (m-80) REVERT: G 102 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.6504 (mpp-170) REVERT: H 92 GLU cc_start: 0.7626 (tp30) cc_final: 0.7366 (tp30) REVERT: I 60 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.5119 (mm-30) REVERT: I 121 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7346 (mp) REVERT: I 140 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.6539 (pptt) outliers start: 101 outliers final: 66 residues processed: 274 average time/residue: 0.5384 time to fit residues: 172.7054 Evaluate side-chains 270 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 190 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 123 ARG 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 51 GLU 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 99 LYS Chi-restraints excluded: chain D residue 108 THR 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 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 46 THR Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 80 THR 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 11 PHE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 112 SER 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 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 117 VAL Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain H residue 186 SER 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 60 GLU 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 146 LEU Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 18 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 113 optimal weight: 6.9990 chunk 11 optimal weight: 50.0000 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.225125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.189653 restraints weight = 34492.401| |-----------------------------------------------------------------------------| r_work (start): 0.4242 rms_B_bonded: 1.94 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4241 r_free = 0.4241 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4241 r_free = 0.4241 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24861 Z= 0.150 Angle : 0.526 12.386 35516 Z= 0.289 Chirality : 0.037 0.193 4378 Planarity : 0.005 0.057 3276 Dihedral : 22.425 165.008 8284 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 6.86 % Allowed : 36.38 % Favored : 56.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.18), residues: 2191 helix: 1.00 (0.14), residues: 1418 sheet: -2.77 (0.37), residues: 95 loop : -1.84 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 123 TYR 0.024 0.002 TYR F 17 PHE 0.020 0.002 PHE G 180 TRP 0.018 0.003 TRP E 166 HIS 0.015 0.002 HIS J 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (24861) covalent geometry : angle 0.52574 / 0.29 (35516) hydrogen bonds : bond 0.04790 / 3.62 ( 1335) hydrogen bonds : angle 3.98439 / 3.02 ( 3578) ********************** REFINEMENT MACRO_CYCLE 10 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 286 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 194 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 114 SER cc_start: 0.6396 (m) cc_final: 0.6167 (p) REVERT: C 123 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.6158 (ttp80) REVERT: C 130 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6685 (tt0) REVERT: D 11 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5242 (p90) REVERT: D 38 SER cc_start: 0.6632 (t) cc_final: 0.6376 (m) REVERT: D 51 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.5789 (mp0) REVERT: D 78 GLN cc_start: 0.7783 (OUTLIER) cc_final: 0.7322 (pt0) REVERT: E 41 GLU cc_start: 0.5921 (OUTLIER) cc_final: 0.5229 (tp30) REVERT: E 55 ILE cc_start: 0.6544 (mt) cc_final: 0.6263 (mp) REVERT: E 106 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: E 175 ILE cc_start: 0.6820 (OUTLIER) cc_final: 0.6534 (tp) REVERT: F 109 ARG cc_start: 0.7322 (OUTLIER) cc_final: 0.5400 (mtt180) REVERT: G 11 PHE cc_start: 0.6564 (OUTLIER) cc_final: 0.5804 (m-80) REVERT: G 102 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.6734 (mpp-170) REVERT: I 60 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.5145 (mm-30) REVERT: I 88 GLU cc_start: 0.7026 (OUTLIER) cc_final: 0.6813 (mt-10) REVERT: I 121 ILE cc_start: 0.7761 (OUTLIER) cc_final: 0.7370 (mp) REVERT: I 140 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.6471 (pptt) outliers start: 92 outliers final: 65 residues processed: 269 average time/residue: 0.5865 time to fit residues: 184.5416 Evaluate side-chains 269 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 189 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL 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 123 ARG 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 51 GLU 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 99 LYS Chi-restraints excluded: chain D residue 108 THR 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 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 46 THR Chi-restraints excluded: chain E residue 106 GLU 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 175 ILE Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 73 SER Chi-restraints excluded: chain F residue 80 THR 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 11 PHE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 112 SER 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 186 SER 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 H residue 186 SER Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 80 THR Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 88 GLU 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 146 LEU Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 18 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 143 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 9 optimal weight: 40.0000 chunk 111 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.224205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.188018 restraints weight = 32968.143| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 1.86 r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4225 r_free = 0.4225 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 24861 Z= 0.175 Angle : 0.559 15.657 35516 Z= 0.304 Chirality : 0.038 0.189 4378 Planarity : 0.005 0.057 3276 Dihedral : 22.431 164.796 8282 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 7.31 % Allowed : 36.01 % Favored : 56.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 2191 helix: 0.90 (0.14), residues: 1418 sheet: -2.77 (0.40), residues: 83 loop : -1.85 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 123 TYR 0.025 0.002 TYR F 17 PHE 0.021 0.002 PHE G 180 TRP 0.017 0.004 TRP E 166 HIS 0.010 0.002 HIS E 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 (24861) covalent geometry : angle 0.55851 / 0.30 (35516) hydrogen bonds : bond 0.05026 / 3.80 ( 1335) hydrogen bonds : angle 4.05010 / 3.07 ( 3578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7407.14 seconds wall clock time: 126 minutes 52.38 seconds (7612.38 seconds total)