Starting phenix.real_space_refine on Sun Aug 24 21:10:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kd9_37128/08_2025/8kd9_37128.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kd9_37128/08_2025/8kd9_37128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kd9_37128/08_2025/8kd9_37128.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kd9_37128/08_2025/8kd9_37128.map" model { file = "/net/cci-nas-00/data/ceres_data/8kd9_37128/08_2025/8kd9_37128.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kd9_37128/08_2025/8kd9_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-2.0-5787/lib/python3.9/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: 5.89, per 1000 atoms: 0.25 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 698.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 3.25 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: 3.35 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5103 1.33 - 1.45: 7133 1.45 - 1.57: 11823 1.57 - 1.69: 720 1.69 - 1.81: 82 Bond restraints: 24861 Sorted by residual: bond pdb=" N ASN A 13 " pdb=" CA ASN A 13 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.16e-02 7.43e+03 8.37e+00 bond pdb=" N ILE H 32 " pdb=" CA ILE H 32 " ideal model delta sigma weight residual 1.462 1.493 -0.031 1.14e-02 7.69e+03 7.34e+00 bond pdb=" N ILE J 97 " pdb=" CA ILE J 97 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.32e+00 bond pdb=" N ARG J 96 " pdb=" CA ARG J 96 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.17e-02 7.31e+03 7.17e+00 bond pdb=" N GLU J 91 " pdb=" CA GLU J 91 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.18e-02 7.18e+03 7.02e+00 ... (remaining 24856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 34971 2.02 - 4.04: 489 4.04 - 6.06: 46 6.06 - 8.08: 9 8.08 - 10.10: 1 Bond angle restraints: 35516 Sorted by residual: angle pdb=" N VAL A 10 " pdb=" CA VAL A 10 " pdb=" C VAL A 10 " ideal model delta sigma weight residual 113.71 107.69 6.02 9.50e-01 1.11e+00 4.01e+01 angle pdb=" C GLU F 22 " pdb=" CA GLU F 22 " pdb=" CB GLU F 22 " ideal model delta sigma weight residual 115.79 109.71 6.08 1.19e+00 7.06e-01 2.61e+01 angle pdb=" N GLY I 59 " pdb=" CA GLY I 59 " pdb=" C GLY I 59 " ideal model delta sigma weight residual 111.67 115.45 -3.78 9.20e-01 1.18e+00 1.69e+01 angle pdb=" C GLU H 21 " pdb=" CA GLU H 21 " pdb=" CB GLU H 21 " ideal model delta sigma weight residual 115.89 110.66 5.23 1.32e+00 5.74e-01 1.57e+01 angle pdb=" CA GLU C 185 " pdb=" CB GLU C 185 " pdb=" CG GLU C 185 " ideal model delta sigma weight residual 114.10 121.88 -7.78 2.00e+00 2.50e-01 1.51e+01 ... (remaining 35511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.45: 13883 34.45 - 68.90: 1547 68.90 - 103.35: 203 103.35 - 137.79: 1 137.79 - 172.24: 2 Dihedral angle restraints: 15636 sinusoidal: 9125 harmonic: 6511 Sorted by residual: dihedral pdb=" C4' U T 60 " pdb=" C3' U T 60 " pdb=" C2' U T 60 " pdb=" C1' U T 60 " ideal model delta sinusoidal sigma weight residual -35.00 34.45 -69.45 1 8.00e+00 1.56e-02 9.73e+01 dihedral pdb=" C5' U T 60 " pdb=" C4' U T 60 " pdb=" C3' U T 60 " pdb=" O3' U T 60 " ideal model delta sinusoidal sigma weight residual 147.00 81.50 65.50 1 8.00e+00 1.56e-02 8.78e+01 dihedral pdb=" O4' U T 60 " pdb=" C4' U T 60 " pdb=" C3' U T 60 " pdb=" C2' U T 60 " ideal model delta sinusoidal sigma weight residual 24.00 -34.35 58.35 1 8.00e+00 1.56e-02 7.13e+01 ... (remaining 15633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3938 0.061 - 0.122: 415 0.122 - 0.183: 19 0.183 - 0.245: 5 0.245 - 0.306: 1 Chirality restraints: 4378 Sorted by residual: chirality pdb=" C3' U T 60 " pdb=" C4' U T 60 " pdb=" O3' U T 60 " pdb=" C2' U T 60 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C2' U T 60 " pdb=" C3' U T 60 " pdb=" O2' U T 60 " pdb=" C1' U T 60 " both_signs ideal model delta sigma weight residual False -2.52 -2.74 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA ILE H 32 " pdb=" N ILE H 32 " pdb=" C ILE H 32 " pdb=" CB ILE H 32 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 4375 not shown) Planarity restraints: 3276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER J 73 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.68e+00 pdb=" N PRO J 74 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO J 74 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 74 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 73 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO D 74 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO D 74 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 74 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 81 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO G 82 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO G 82 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 82 " 0.032 5.00e-02 4.00e+02 ... (remaining 3273 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2649 2.74 - 3.28: 23269 3.28 - 3.82: 47266 3.82 - 4.36: 53530 4.36 - 4.90: 79791 Nonbonded interactions: 206505 Sorted by model distance: nonbonded pdb=" O6 G N 26 " pdb=" N1 A N 44 " model vdw 2.203 2.496 nonbonded pdb=" OH TYR G 49 " pdb=" OE2 GLU G 66 " model vdw 2.216 3.040 nonbonded pdb=" NH2 ARG H 109 " pdb=" O3' C T 56 " model vdw 2.228 3.120 nonbonded pdb=" O2' U T 16 " pdb=" OP2 G T 19 " model vdw 2.231 3.040 nonbonded pdb=" O2' G M 15 " pdb=" O6 G M 20 " model vdw 2.232 3.040 ... (remaining 206500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 20 or resid 26 through 57 or resid 61 through 12 \ 8 or resid 130 through 187)) selection = (chain 'B' and (resid 3 through 16 or resid 18 through 20 or resid 26 through 57 \ or resid 61 through 128 or resid 130 through 187)) selection = (chain 'C' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'F' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'G' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'H' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'I' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'J' and ((resid 3 through 13 and (name N or name CA or name C or name O o \ r name CB )) or resid 14 or (resid 15 through 16 and (name N or name CA or name \ C or name O or name CB )) or (resid 18 through 20 and (name N or name CA or name \ C or name O or name CB )) or (resid 26 through 44 and (name N or name CA or nam \ e C or name O or name CB )) or resid 45 or (resid 46 through 57 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 61 through 73 and (name N or \ name CA or name C or name O or name CB )) or resid 74 or (resid 75 through 81 an \ d (name N or name CA or name C or name O or name CB )) or resid 82 through 83 or \ (resid 84 through 99 and (name N or name CA or name C or name O or name CB )) o \ r resid 100 or (resid 101 through 112 and (name N or name CA or name C or name O \ or name CB )) or resid 113 or (resid 114 through 117 and (name N or name CA or \ name C or name O or name CB )) or resid 118 or (resid 119 through 128 and (name \ N or name CA or name C or name O or name CB )) or (resid 130 through 134 and (na \ me N or name CA or name C or name O or name CB )) or resid 135 or (resid 136 thr \ ough 153 and (name N or name CA or name C or name O or name CB )) or resid 154 o \ r (resid 155 through 161 and (name N or name CA or name C or name O or name CB ) \ ) or resid 162 or (resid 163 through 170 and (name N or name CA or name C or nam \ e O or name CB )) or resid 171 or (resid 172 through 176 and (name N or name CA \ or name C or name O or name CB )) or resid 177 or (resid 178 through 187 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'K' and (resid 3 through 16 or resid 18 through 20 or resid 26 through 57 \ or resid 61 through 128 or resid 130 through 187)) selection = (chain 'L' and (resid 3 through 16 or resid 18 through 128 or resid 130 through \ 187)) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.31 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 22.050 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 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:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24861 Z= 0.142 Angle : 0.579 10.097 35516 Z= 0.320 Chirality : 0.037 0.306 4378 Planarity : 0.004 0.060 3276 Dihedral : 23.781 172.242 11392 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 8.49 % Allowed : 34.61 % Favored : 56.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren 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 covalent geometry : bond 0.00267 (24861) covalent geometry : angle 0.57876 (35516) hydrogen bonds : bond 0.12967 ( 1335) hydrogen bonds : angle 5.44389 ( 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 : 0.589 Fit side-chains revert: symmetry clash REVERT: C 185 GLU cc_start: 0.5322 (tm-30) cc_final: 0.4229 (mm-30) REVERT: D 11 PHE cc_start: 0.5930 (OUTLIER) cc_final: 0.5490 (p90) REVERT: E 119 LYS cc_start: 0.7564 (pttt) cc_final: 0.6995 (pptt) REVERT: F 51 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7392 (mm-30) REVERT: G 175 ILE cc_start: 0.7071 (OUTLIER) cc_final: 0.6739 (tp) REVERT: I 151 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6940 (pt0) REVERT: J 54 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.6914 (mtmt) outliers start: 114 outliers final: 95 residues processed: 319 average time/residue: 0.5024 time to fit residues: 187.2604 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 : 0.699 ------------------------------------------------------------------------------- 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: 10.0000 chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 20.0000 chunk 227 optimal weight: 8.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 50.0000 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 40.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN J 33 HIS J 98 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.227146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.191451 restraints weight = 34836.560| |-----------------------------------------------------------------------------| r_work (start): 0.4261 rms_B_bonded: 1.98 r_work (final): 0.4261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4261 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4261 r_free = 0.4261 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4261 r_free = 0.4261 target_work(ls_wunit_k1) = 0.189 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4261 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24861 Z= 0.125 Angle : 0.540 9.326 35516 Z= 0.277 Chirality : 0.036 0.225 4378 Planarity : 0.005 0.065 3276 Dihedral : 22.795 163.491 8398 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 9.00 % Allowed : 31.00 % Favored : 60.00 % 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 aren not related in a simple way. whole: -0.19 (0.18), residues: 2191 helix: 0.89 (0.14), residues: 1413 sheet: -2.66 (0.39), residues: 99 loop : -1.84 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 109 TYR 0.029 0.002 TYR J 17 PHE 0.016 0.002 PHE E 65 TRP 0.020 0.003 TRP E 166 HIS 0.017 0.002 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00270 (24861) covalent geometry : angle 0.53974 (35516) hydrogen bonds : bond 0.04258 ( 1335) hydrogen bonds : angle 4.03463 ( 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 331 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 210 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: D 11 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5724 (p90) REVERT: D 78 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7272 (pt0) REVERT: D 176 ASP cc_start: 0.6246 (OUTLIER) cc_final: 0.6028 (p0) REVERT: E 41 GLU cc_start: 0.5834 (OUTLIER) cc_final: 0.5135 (tp30) REVERT: E 106 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6317 (mp0) REVERT: F 109 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.5283 (mpt-90) REVERT: H 91 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6907 (tt0) REVERT: I 60 GLU cc_start: 0.5571 (OUTLIER) cc_final: 0.5063 (mm-30) REVERT: I 121 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7341 (mp) outliers start: 121 outliers final: 54 residues processed: 309 average time/residue: 0.5366 time to fit residues: 192.7577 Evaluate side-chains 260 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 197 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 47 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 2 ASP Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 13 ASN Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 178 LYS Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 73 SER Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 70 LYS Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain I residue 60 GLU Chi-restraints excluded: chain I residue 84 ASP Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 132 LEU Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 151 GLU Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 178 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 94 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 198 optimal weight: 30.0000 chunk 35 optimal weight: 0.0470 chunk 123 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 131 optimal weight: 0.3980 overall best weight: 1.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 ASN D 179 ASN E 24 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.225792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.192793 restraints weight = 38794.598| |-----------------------------------------------------------------------------| r_work (start): 0.4275 rms_B_bonded: 1.95 r_work (final): 0.4275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4275 r_free = 0.4275 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4275 r_free = 0.4275 target_work(ls_wunit_k1) = 0.190 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6542 moved from start: 0.1367 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= 0.139 Angle : 0.545 10.405 35516 Z= 0.279 Chirality : 0.037 0.212 4378 Planarity : 0.005 0.059 3276 Dihedral : 22.586 162.604 8304 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 9.96 % Allowed : 30.41 % Favored : 59.63 % 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 aren not related in a simple way. whole: -0.07 (0.18), residues: 2191 helix: 1.00 (0.14), residues: 1423 sheet: -2.83 (0.38), residues: 99 loop : -1.84 (0.22), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 102 TYR 0.025 0.002 TYR J 17 PHE 0.015 0.002 PHE G 180 TRP 0.019 0.003 TRP E 166 HIS 0.016 0.002 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00315 (24861) covalent geometry : angle 0.54508 (35516) hydrogen bonds : bond 0.04369 ( 1335) hydrogen bonds : angle 3.93632 ( 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 340 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 206 time to evaluate : 0.514 Fit side-chains REVERT: C 117 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7229 (p) REVERT: C 130 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6738 (tt0) REVERT: D 11 PHE cc_start: 0.6027 (OUTLIER) cc_final: 0.5400 (p90) REVERT: D 38 SER cc_start: 0.6456 (t) cc_final: 0.6148 (m) REVERT: D 55 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.7099 (mp) REVERT: D 78 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7358 (pt0) REVERT: E 41 GLU cc_start: 0.5913 (OUTLIER) cc_final: 0.5223 (tp30) REVERT: E 55 ILE cc_start: 0.6399 (mt) cc_final: 0.6144 (mp) REVERT: E 106 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: F 109 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.5010 (mpt-90) REVERT: G 11 PHE cc_start: 0.6422 (OUTLIER) cc_final: 0.5620 (m-80) REVERT: G 102 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.6455 (mpp-170) REVERT: H 71 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.8043 (mt) REVERT: I 121 ILE cc_start: 0.7718 (OUTLIER) cc_final: 0.7319 (mp) outliers start: 134 outliers final: 59 residues processed: 309 average time/residue: 0.5668 time to fit residues: 203.2390 Evaluate side-chains 264 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 193 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 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 55 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 11 PHE Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 67 MET Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain G residue 170 ILE Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 37 ASN Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 71 ILE Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain I residue 8 THR 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 146 LEU Chi-restraints excluded: chain I residue 170 ILE 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 178 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 113 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 249 optimal weight: 10.0000 chunk 52 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 7.9990 chunk 216 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 208 optimal weight: 20.0000 chunk 182 optimal weight: 50.0000 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 ASN D 179 ASN E 24 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.223156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.186026 restraints weight = 32442.067| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 1.89 r_work (final): 0.4203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4203 r_free = 0.4203 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4203 r_free = 0.4203 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 24861 Z= 0.203 Angle : 0.614 11.784 35516 Z= 0.314 Chirality : 0.039 0.219 4378 Planarity : 0.005 0.062 3276 Dihedral : 22.611 161.740 8284 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 9.74 % Allowed : 30.77 % Favored : 59.48 % 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 aren not related in a simple way. whole: -0.29 (0.18), residues: 2191 helix: 0.80 (0.14), residues: 1412 sheet: -2.74 (0.40), residues: 93 loop : -1.86 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 125 TYR 0.025 0.002 TYR F 17 PHE 0.023 0.002 PHE G 180 TRP 0.021 0.004 TRP E 166 HIS 0.016 0.002 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00473 (24861) covalent geometry : angle 0.61415 (35516) hydrogen bonds : bond 0.05007 ( 1335) hydrogen bonds : angle 4.12883 ( 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 335 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 204 time to evaluate : 0.711 Fit side-chains revert: symmetry clash REVERT: C 130 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6624 (tt0) REVERT: D 11 PHE cc_start: 0.6136 (OUTLIER) cc_final: 0.5331 (p90) REVERT: D 38 SER cc_start: 0.6778 (t) cc_final: 0.6506 (m) REVERT: D 78 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7408 (pt0) REVERT: E 41 GLU cc_start: 0.6023 (OUTLIER) cc_final: 0.5361 (tp30) REVERT: E 55 ILE cc_start: 0.6499 (mt) cc_final: 0.6241 (mp) REVERT: E 106 GLU cc_start: 0.7261 (OUTLIER) cc_final: 0.6366 (mp0) REVERT: E 179 ASN cc_start: 0.6374 (OUTLIER) cc_final: 0.5971 (m110) REVERT: F 109 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.4989 (mpt-90) REVERT: G 11 PHE cc_start: 0.6630 (OUTLIER) cc_final: 0.5736 (m-80) REVERT: G 102 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.6536 (mpp-170) REVERT: I 60 GLU cc_start: 0.5608 (OUTLIER) cc_final: 0.5227 (mm-30) REVERT: I 121 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7479 (mp) REVERT: I 176 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.6354 (p0) REVERT: J 92 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6759 (tt0) outliers start: 131 outliers final: 66 residues processed: 310 average time/residue: 0.5575 time to fit residues: 199.7484 Evaluate side-chains 276 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 197 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 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 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 106 GLU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain D residue 170 ILE Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 109 ARG Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 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 37 ASN Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 54 LYS 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 I residue 176 ASP 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: 0.5980 chunk 40 optimal weight: 0.8980 chunk 225 optimal weight: 30.0000 chunk 147 optimal weight: 6.9990 chunk 1 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 206 optimal weight: 20.0000 chunk 193 optimal weight: 20.0000 chunk 240 optimal weight: 50.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 ASN E 24 GLN ** E 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 33 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.222117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.186647 restraints weight = 34501.485| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 1.92 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4210 r_free = 0.4210 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4210 r_free = 0.4210 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 24861 Z= 0.227 Angle : 0.646 13.097 35516 Z= 0.332 Chirality : 0.040 0.224 4378 Planarity : 0.005 0.060 3276 Dihedral : 22.656 161.472 8284 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 10.70 % Allowed : 30.33 % Favored : 58.97 % 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 aren not related in a simple way. whole: -0.56 (0.18), residues: 2191 helix: 0.60 (0.14), residues: 1404 sheet: -2.95 (0.38), residues: 93 loop : -1.97 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 123 TYR 0.026 0.002 TYR F 17 PHE 0.020 0.003 PHE G 180 TRP 0.023 0.004 TRP E 166 HIS 0.014 0.002 HIS E 33 Details of bonding type rmsd covalent geometry : bond 0.00530 (24861) covalent geometry : angle 0.64648 (35516) hydrogen bonds : bond 0.05307 ( 1335) hydrogen bonds : angle 4.26228 ( 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 347 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 203 time to evaluate : 0.760 Fit side-chains REVERT: C 130 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6575 (tt0) REVERT: D 11 PHE cc_start: 0.6031 (OUTLIER) cc_final: 0.5332 (p90) REVERT: D 29 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.5468 (tm-30) REVERT: D 78 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7479 (pt0) REVERT: E 41 GLU cc_start: 0.6063 (OUTLIER) cc_final: 0.5387 (tp30) REVERT: E 106 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: E 179 ASN cc_start: 0.6615 (OUTLIER) cc_final: 0.6293 (m110) REVERT: F 109 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.5070 (mpt-90) REVERT: F 178 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5692 (mppt) REVERT: G 11 PHE cc_start: 0.6582 (OUTLIER) cc_final: 0.5827 (m-80) REVERT: G 102 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.6652 (mpp-170) REVERT: I 60 GLU cc_start: 0.5568 (OUTLIER) cc_final: 0.5161 (mm-30) REVERT: I 121 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7527 (mp) REVERT: I 175 ILE cc_start: 0.6655 (OUTLIER) cc_final: 0.6384 (tt) REVERT: I 176 ASP cc_start: 0.6922 (OUTLIER) cc_final: 0.6432 (p0) REVERT: J 92 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6751 (tt0) outliers start: 144 outliers final: 73 residues processed: 319 average time/residue: 0.5955 time to fit residues: 219.9810 Evaluate side-chains 282 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 193 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 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 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 41 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 99 LYS 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 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 60 GLU Chi-restraints excluded: chain F residue 68 VAL 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 178 LYS 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 163 LEU Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 11 PHE 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 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 54 LYS Chi-restraints excluded: chain I residue 56 MET 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 163 LEU Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain J residue 2 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 105 optimal weight: 2.9990 chunk 149 optimal weight: 0.2980 chunk 129 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 190 optimal weight: 40.0000 chunk 74 optimal weight: 0.7980 chunk 11 optimal weight: 50.0000 chunk 46 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 212 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 ASN C 33 HIS E 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 = 0.4633 r_free = 0.4633 target = 0.228111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.191631 restraints weight = 31126.284| |-----------------------------------------------------------------------------| r_work (start): 0.4259 rms_B_bonded: 1.80 r_work: 0.3891 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3866 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3866 r_free = 0.3866 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3866 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 24861 Z= 0.112 Angle : 0.529 11.181 35516 Z= 0.270 Chirality : 0.036 0.209 4378 Planarity : 0.005 0.060 3276 Dihedral : 22.353 162.576 8283 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 7.45 % Allowed : 34.17 % Favored : 58.38 % 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 aren not related in a simple way. whole: 0.02 (0.18), residues: 2191 helix: 1.07 (0.14), residues: 1411 sheet: -2.81 (0.39), residues: 99 loop : -1.78 (0.22), residues: 681 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 0.039 0.002 PHE C 11 TRP 0.023 0.003 TRP G 166 HIS 0.013 0.002 HIS H 33 Details of bonding type rmsd covalent geometry : bond 0.00241 (24861) covalent geometry : angle 0.52860 (35516) hydrogen bonds : bond 0.03957 ( 1335) hydrogen bonds : angle 3.87037 ( 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 305 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 205 time to evaluate : 0.665 Fit side-chains REVERT: C 49 TYR cc_start: 0.7377 (t80) cc_final: 0.7100 (t80) REVERT: C 117 VAL cc_start: 0.7541 (t) cc_final: 0.7216 (p) REVERT: C 130 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: D 11 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.4759 (p90) REVERT: D 33 HIS cc_start: 0.5471 (OUTLIER) cc_final: 0.5257 (m-70) REVERT: D 141 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7146 (pt0) REVERT: E 41 GLU cc_start: 0.6368 (OUTLIER) cc_final: 0.5799 (tp30) REVERT: E 55 ILE cc_start: 0.6688 (mt) cc_final: 0.6440 (mp) REVERT: E 106 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: F 51 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7539 (mm-30) REVERT: H 91 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7708 (tt0) REVERT: I 121 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7428 (mp) outliers start: 100 outliers final: 41 residues processed: 289 average time/residue: 0.5010 time to fit residues: 168.2651 Evaluate side-chains 240 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 17 TYR Chi-restraints excluded: chain D residue 33 HIS 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 93 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 54 LYS Chi-restraints excluded: chain G residue 148 LEU Chi-restraints excluded: chain G residue 157 VAL Chi-restraints excluded: chain G residue 163 LEU Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 175 ILE Chi-restraints excluded: chain I residue 8 THR 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 146 LEU Chi-restraints excluded: chain I residue 170 ILE 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 132 LEU Chi-restraints excluded: chain J residue 175 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 18 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 211 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 59 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 ASN E 24 GLN F 179 ASN H 24 GLN J 33 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4590 r_free = 0.4590 target = 0.223572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.188306 restraints weight = 32754.083| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 1.87 r_work (final): 0.4226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4226 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4226 r_free = 0.4226 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4226 r_free = 0.4226 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24861 Z= 0.197 Angle : 0.612 12.551 35516 Z= 0.313 Chirality : 0.039 0.244 4378 Planarity : 0.005 0.056 3276 Dihedral : 22.414 162.889 8263 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 8.34 % Allowed : 33.80 % Favored : 57.86 % 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 aren not related in a simple way. whole: -0.25 (0.18), residues: 2191 helix: 0.83 (0.14), residues: 1418 sheet: -2.71 (0.41), residues: 93 loop : -1.88 (0.22), residues: 680 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 0.024 0.002 PHE C 11 TRP 0.020 0.004 TRP E 166 HIS 0.016 0.003 HIS H 33 Details of bonding type rmsd covalent geometry : bond 0.00459 (24861) covalent geometry : angle 0.61168 (35516) hydrogen bonds : bond 0.04854 ( 1335) hydrogen bonds : angle 4.06901 ( 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 312 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 200 time to evaluate : 0.784 Fit side-chains REVERT: C 130 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6674 (tt0) REVERT: D 11 PHE cc_start: 0.5890 (OUTLIER) cc_final: 0.5335 (p90) REVERT: D 29 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.5656 (tm-30) REVERT: D 78 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7371 (pt0) REVERT: E 41 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5369 (tp30) REVERT: E 55 ILE cc_start: 0.6585 (mt) cc_final: 0.6303 (mp) REVERT: E 106 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: E 179 ASN cc_start: 0.6496 (OUTLIER) cc_final: 0.6245 (m110) REVERT: G 11 PHE cc_start: 0.6614 (OUTLIER) cc_final: 0.5843 (m-80) REVERT: G 102 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.6488 (mpp-170) REVERT: H 92 GLU cc_start: 0.7650 (tp30) cc_final: 0.7404 (tp30) REVERT: I 121 ILE cc_start: 0.7830 (OUTLIER) cc_final: 0.7545 (mp) REVERT: I 140 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6361 (pptt) REVERT: I 175 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6248 (tt) REVERT: I 176 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6295 (p0) REVERT: J 52 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7156 (ttp) outliers start: 112 outliers final: 51 residues processed: 290 average time/residue: 0.5365 time to fit residues: 180.4065 Evaluate side-chains 263 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 198 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 170 ILE 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 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 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 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 106 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL 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 72 ARG Chi-restraints excluded: chain G residue 102 ARG 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 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 80 THR Chi-restraints excluded: chain I residue 121 ILE 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 I residue 175 ILE Chi-restraints excluded: chain I residue 176 ASP Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 52 MET Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 132 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 140 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 209 optimal weight: 40.0000 chunk 106 optimal weight: 0.9980 chunk 243 optimal weight: 20.0000 chunk 52 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 179 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 183 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.4631 r_free = 0.4631 target = 0.227992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.196538 restraints weight = 35081.086| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 1.81 r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4315 r_free = 0.4315 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4315 r_free = 0.4315 target_work(ls_wunit_k1) = 0.195 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24861 Z= 0.113 Angle : 0.528 11.739 35516 Z= 0.271 Chirality : 0.036 0.198 4378 Planarity : 0.005 0.059 3276 Dihedral : 22.222 162.922 8263 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.94 % Allowed : 35.35 % Favored : 57.71 % 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 aren not related in a simple way. whole: 0.08 (0.18), residues: 2191 helix: 1.13 (0.14), residues: 1425 sheet: -2.76 (0.38), residues: 95 loop : -1.84 (0.22), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 123 TYR 0.023 0.002 TYR F 17 PHE 0.014 0.001 PHE C 11 TRP 0.023 0.003 TRP G 166 HIS 0.020 0.003 HIS H 33 Details of bonding type rmsd covalent geometry : bond 0.00249 (24861) covalent geometry : angle 0.52815 (35516) hydrogen bonds : bond 0.03914 ( 1335) hydrogen bonds : angle 3.83143 ( 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 298 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 205 time to evaluate : 0.790 Fit side-chains REVERT: C 117 VAL cc_start: 0.7454 (t) cc_final: 0.7225 (p) REVERT: C 130 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6554 (tm-30) REVERT: D 11 PHE cc_start: 0.5838 (OUTLIER) cc_final: 0.5062 (p90) REVERT: D 78 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7314 (pt0) REVERT: E 41 GLU cc_start: 0.5854 (OUTLIER) cc_final: 0.5171 (tp30) REVERT: E 106 GLU cc_start: 0.7101 (OUTLIER) cc_final: 0.6474 (mp0) REVERT: F 130 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6504 (tt0) REVERT: H 91 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7184 (tt0) REVERT: I 60 GLU cc_start: 0.5618 (OUTLIER) cc_final: 0.5122 (mm-30) REVERT: I 121 ILE cc_start: 0.7692 (OUTLIER) cc_final: 0.7357 (mp) REVERT: I 175 ILE cc_start: 0.6126 (OUTLIER) cc_final: 0.5701 (tt) outliers start: 93 outliers final: 43 residues processed: 278 average time/residue: 0.5965 time to fit residues: 191.6672 Evaluate side-chains 244 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 78 GLN Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 148 LEU Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain G residue 8 THR Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 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 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 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 146 LEU Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 84 ASP Chi-restraints excluded: chain J residue 175 ILE 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: 9.9990 chunk 197 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 12 optimal weight: 20.0000 chunk 152 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 246 optimal weight: 40.0000 chunk 165 optimal weight: 0.0980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 ASN J 33 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.223714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.188305 restraints weight = 34306.279| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 1.92 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4229 r_free = 0.4229 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 = 0.4229 r_free = 0.4229 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 24861 Z= 0.199 Angle : 0.621 12.862 35516 Z= 0.317 Chirality : 0.039 0.210 4378 Planarity : 0.005 0.056 3276 Dihedral : 22.330 162.491 8254 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 6.13 % Allowed : 36.24 % Favored : 57.64 % 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 aren not related in a simple way. whole: -0.20 (0.18), residues: 2191 helix: 0.88 (0.14), residues: 1420 sheet: -2.67 (0.38), residues: 105 loop : -1.86 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 123 TYR 0.025 0.002 TYR F 17 PHE 0.018 0.002 PHE H 31 TRP 0.019 0.004 TRP E 166 HIS 0.023 0.003 HIS H 33 Details of bonding type rmsd covalent geometry : bond 0.00466 (24861) covalent geometry : angle 0.62062 (35516) hydrogen bonds : bond 0.04796 ( 1335) hydrogen bonds : angle 4.04309 ( 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 278 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 196 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: C 130 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6670 (tt0) REVERT: D 11 PHE cc_start: 0.5933 (OUTLIER) cc_final: 0.5353 (p90) REVERT: D 78 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7369 (pt0) REVERT: E 41 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5473 (tp30) REVERT: E 106 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: E 179 ASN cc_start: 0.6533 (OUTLIER) cc_final: 0.6312 (m110) REVERT: H 51 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: H 127 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7579 (mtpm) REVERT: I 121 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7548 (mp) REVERT: I 175 ILE cc_start: 0.6463 (OUTLIER) cc_final: 0.6235 (tt) outliers start: 82 outliers final: 48 residues processed: 259 average time/residue: 0.5511 time to fit residues: 167.0871 Evaluate side-chains 251 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 194 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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 130 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 163 LEU 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 78 GLN Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 170 ILE 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 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 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 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 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 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 I residue 175 ILE Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 84 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 113 optimal weight: 0.9990 chunk 11 optimal weight: 40.0000 chunk 84 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 0 optimal weight: 40.0000 chunk 1 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN ** E 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 = 0.4613 r_free = 0.4613 target = 0.226018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.193879 restraints weight = 34386.983| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 1.80 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4290 r_free = 0.4290 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4290 r_free = 0.4290 target_work(ls_wunit_k1) = 0.192 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24861 Z= 0.137 Angle : 0.563 12.745 35516 Z= 0.287 Chirality : 0.037 0.200 4378 Planarity : 0.005 0.059 3276 Dihedral : 22.244 162.468 8254 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.80 % Allowed : 37.64 % Favored : 57.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.18), residues: 2191 helix: 1.06 (0.14), residues: 1420 sheet: -2.72 (0.38), residues: 95 loop : -1.84 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 18 TYR 0.024 0.002 TYR F 17 PHE 0.020 0.002 PHE F 180 TRP 0.021 0.003 TRP G 166 HIS 0.019 0.003 HIS H 33 Details of bonding type rmsd covalent geometry : bond 0.00312 (24861) covalent geometry : angle 0.56269 (35516) hydrogen bonds : bond 0.04172 ( 1335) hydrogen bonds : angle 3.93213 ( 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 258 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 194 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: C 117 VAL cc_start: 0.7510 (t) cc_final: 0.7266 (p) REVERT: C 130 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: D 11 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.5244 (m-80) REVERT: D 28 MET cc_start: 0.5060 (tpt) cc_final: 0.4756 (tpt) REVERT: D 78 GLN cc_start: 0.7768 (OUTLIER) cc_final: 0.7327 (pt0) REVERT: E 41 GLU cc_start: 0.5960 (OUTLIER) cc_final: 0.5312 (tp30) REVERT: E 106 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6541 (mp0) REVERT: H 127 LYS cc_start: 0.7841 (mtpt) cc_final: 0.7568 (mtpm) REVERT: I 121 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7415 (mp) REVERT: I 175 ILE cc_start: 0.6210 (OUTLIER) cc_final: 0.6010 (tt) outliers start: 64 outliers final: 42 residues processed: 244 average time/residue: 0.5320 time to fit residues: 151.5247 Evaluate side-chains 240 residues out of total 1976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 191 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain D residue 12 THR 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 99 LYS Chi-restraints excluded: chain D residue 143 VAL Chi-restraints excluded: chain E residue 8 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 106 GLU Chi-restraints excluded: chain E residue 121 ILE Chi-restraints excluded: chain E residue 151 GLU Chi-restraints excluded: chain E residue 179 ASN Chi-restraints excluded: chain F residue 12 THR Chi-restraints excluded: chain F residue 68 VAL 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 112 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 8 THR Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 51 GLU 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 80 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 170 ILE Chi-restraints excluded: chain I residue 175 ILE Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 84 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 143 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 40.0000 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN ** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.224792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.188358 restraints weight = 32830.317| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 1.94 r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4227 r_free = 0.4227 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 = 0.4227 r_free = 0.4227 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24861 Z= 0.161 Angle : 0.583 12.953 35516 Z= 0.298 Chirality : 0.037 0.195 4378 Planarity : 0.005 0.056 3276 Dihedral : 22.262 162.487 8254 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 5.17 % Allowed : 37.42 % Favored : 57.42 % 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 aren not related in a simple way. whole: -0.10 (0.18), residues: 2191 helix: 0.98 (0.14), residues: 1420 sheet: -2.60 (0.38), residues: 105 loop : -1.87 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 123 TYR 0.028 0.002 TYR J 17 PHE 0.016 0.002 PHE G 180 TRP 0.020 0.004 TRP E 166 HIS 0.020 0.002 HIS H 33 Details of bonding type rmsd covalent geometry : bond 0.00375 (24861) covalent geometry : angle 0.58256 (35516) hydrogen bonds : bond 0.04440 ( 1335) hydrogen bonds : angle 3.97637 ( 3578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7019.27 seconds wall clock time: 120 minutes 16.33 seconds (7216.33 seconds total)