Starting phenix.real_space_refine on Sun Aug 24 00:05:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ch0_30367/08_2025/7ch0_30367.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ch0_30367/08_2025/7ch0_30367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ch0_30367/08_2025/7ch0_30367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ch0_30367/08_2025/7ch0_30367.map" model { file = "/net/cci-nas-00/data/ceres_data/7ch0_30367/08_2025/7ch0_30367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ch0_30367/08_2025/7ch0_30367.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 6 5.49 5 S 68 5.16 5 C 10164 2.51 5 N 2666 2.21 5 O 2952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 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: 15856 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "B" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1995 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 244} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1995 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 244} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1934 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain: "C" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 725 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "F" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 725 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "G" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "H" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "I" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "J" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "K" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1105 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Chain: "L" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1033 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 137} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.43, per 1000 atoms: 0.28 Number of scatterers: 15856 At special positions: 0 Unit cell: (108.7, 105.439, 150.006, 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 68 16.00 P 6 15.00 O 2952 8.00 N 2666 7.00 C 10164 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: 1.04 Conformation dependent library (CDL) restraints added in 712.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3824 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 22 sheets defined 38.9% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 3 through 32 removed outlier: 3.538A pdb=" N SER A 8 " --> pdb=" O ASN A 4 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 52 removed outlier: 3.617A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 77 removed outlier: 3.623A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 70 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.617A pdb=" N TYR A 81 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 86 Processing helix chain 'A' and resid 87 through 98 removed outlier: 4.001A pdb=" N LEU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 126 removed outlier: 3.538A pdb=" N VAL A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 119 " --> pdb=" O ALA A 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 removed outlier: 3.523A pdb=" N GLU A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 144 through 174 removed outlier: 3.586A pdb=" N TRP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Proline residue: A 156 - end of helix removed outlier: 4.034A pdb=" N VAL A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP A 168 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 191 removed outlier: 3.913A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 220 removed outlier: 3.806A pdb=" N LYS A 205 " --> pdb=" O ASN A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 243 removed outlier: 3.868A pdb=" N ILE A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 removed outlier: 3.950A pdb=" N LEU A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.733A pdb=" N ILE B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.795A pdb=" N TYR B 81 " --> pdb=" O ARG B 77 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 124 through 132 removed outlier: 4.013A pdb=" N GLU B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 removed outlier: 3.756A pdb=" N ARG B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 189 removed outlier: 3.681A pdb=" N ILE B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'E' and resid 47 through 55 removed outlier: 3.732A pdb=" N ILE E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.794A pdb=" N TYR E 81 " --> pdb=" O ARG E 77 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR E 82 " --> pdb=" O SER E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 124 through 132 removed outlier: 4.014A pdb=" N GLU E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL E 132 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 157 removed outlier: 3.756A pdb=" N ARG E 152 " --> pdb=" O GLY E 148 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 154 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA E 156 " --> pdb=" O ARG E 152 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 189 removed outlier: 3.680A pdb=" N ILE E 187 " --> pdb=" O LEU E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 211 Processing helix chain 'D' and resid 4 through 32 removed outlier: 3.537A pdb=" N SER D 8 " --> pdb=" O ASN D 4 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU D 9 " --> pdb=" O ALA D 5 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY D 10 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR D 16 " --> pdb=" O LYS D 12 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 27 " --> pdb=" O ALA D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 removed outlier: 3.617A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D 46 " --> pdb=" O PRO D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 77 removed outlier: 3.622A pdb=" N ILE D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 66 " --> pdb=" O SER D 62 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY D 74 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 82 removed outlier: 3.618A pdb=" N TYR D 81 " --> pdb=" O LEU D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 86 Processing helix chain 'D' and resid 87 through 98 removed outlier: 4.001A pdb=" N LEU D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU D 96 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 126 removed outlier: 3.538A pdb=" N VAL D 103 " --> pdb=" O LEU D 99 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 111 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 134 removed outlier: 3.523A pdb=" N GLU D 133 " --> pdb=" O LEU D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 144 through 174 removed outlier: 3.586A pdb=" N TRP D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER D 154 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 155 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Proline residue: D 156 - end of helix removed outlier: 4.034A pdb=" N VAL D 160 " --> pdb=" O PRO D 156 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 191 removed outlier: 3.913A pdb=" N ASN D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 220 removed outlier: 3.805A pdb=" N LYS D 205 " --> pdb=" O ASN D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 243 removed outlier: 3.868A pdb=" N ILE D 231 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 257 removed outlier: 3.950A pdb=" N LEU D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N PHE D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 31 removed outlier: 4.022A pdb=" N MET C 31 " --> pdb=" O PRO C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 62 removed outlier: 5.122A pdb=" N LEU C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU C 58 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N HIS C 60 " --> pdb=" O ALA C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 68 removed outlier: 3.723A pdb=" N LYS C 67 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 31 removed outlier: 4.022A pdb=" N MET F 31 " --> pdb=" O PRO F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 62 removed outlier: 5.121A pdb=" N LEU F 57 " --> pdb=" O GLY F 53 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU F 58 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.723A pdb=" N LYS F 67 " --> pdb=" O ASP F 63 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 28 removed outlier: 4.001A pdb=" N TRP G 9 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N VAL G 10 " --> pdb=" O ASN G 6 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU G 15 " --> pdb=" O GLY G 11 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 152 removed outlier: 3.606A pdb=" N ILE G 147 " --> pdb=" O LEU G 143 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN G 149 " --> pdb=" O ASP G 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 24 removed outlier: 3.658A pdb=" N TRP H 9 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLY H 11 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE H 13 " --> pdb=" O TRP H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 151 Processing helix chain 'I' and resid 8 through 28 removed outlier: 4.015A pdb=" N LEU I 14 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA I 28 " --> pdb=" O VAL I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.694A pdb=" N LEU I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY I 148 " --> pdb=" O GLU I 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 28 removed outlier: 3.796A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE J 13 " --> pdb=" O TRP J 9 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA J 21 " --> pdb=" O ALA J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 removed outlier: 3.526A pdb=" N GLY J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 28 removed outlier: 4.494A pdb=" N PHE K 13 " --> pdb=" O TRP K 9 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 152 removed outlier: 3.618A pdb=" N LEU K 146 " --> pdb=" O VAL K 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 18 removed outlier: 3.700A pdb=" N ALA L 17 " --> pdb=" O PHE L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 28 removed outlier: 4.190A pdb=" N CYS L 25 " --> pdb=" O ALA L 21 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU L 26 " --> pdb=" O LEU L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 152 Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 32 removed outlier: 3.587A pdb=" N VAL B 9 " --> pdb=" O VAL B 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 14 through 18 removed outlier: 3.723A pdb=" N ILE B 27 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N PHE B 16 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP B 25 " --> pdb=" O PHE B 16 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG B 18 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE B 23 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 37 through 39 removed outlier: 6.309A pdb=" N THR B 37 " --> pdb=" O VAL B 200 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 217 through 218 removed outlier: 3.840A pdb=" N ALA B 225 " --> pdb=" O ILE B 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 30 through 32 removed outlier: 3.587A pdb=" N VAL E 9 " --> pdb=" O VAL E 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 14 through 18 removed outlier: 3.723A pdb=" N ILE E 27 " --> pdb=" O VAL E 14 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N PHE E 16 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP E 25 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG E 18 " --> pdb=" O ILE E 23 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE E 23 " --> pdb=" O ARG E 18 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 37 through 39 removed outlier: 6.310A pdb=" N THR E 37 " --> pdb=" O VAL E 200 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 215 through 218 removed outlier: 3.653A pdb=" N ALA E 215 " --> pdb=" O GLY E 227 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY E 227 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA E 225 " --> pdb=" O ILE E 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 9 removed outlier: 3.665A pdb=" N MET C 8 " --> pdb=" O ALA C 15 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 15 " --> pdb=" O MET C 8 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N ARG C 46 " --> pdb=" O LEU C 14 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU C 16 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER C 48 " --> pdb=" O LEU C 16 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N GLY C 18 " --> pdb=" O SER C 48 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL C 50 " --> pdb=" O GLY C 18 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU C 20 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AB2, first strand: chain 'F' and resid 6 through 9 removed outlier: 3.665A pdb=" N MET F 8 " --> pdb=" O ALA F 15 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA F 15 " --> pdb=" O MET F 8 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N ARG F 46 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU F 16 " --> pdb=" O ARG F 46 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER F 48 " --> pdb=" O LEU F 16 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N GLY F 18 " --> pdb=" O SER F 48 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL F 50 " --> pdb=" O GLY F 18 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU F 20 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 41 through 42 Processing sheet with id=AB4, first strand: chain 'G' and resid 39 through 45 removed outlier: 3.588A pdb=" N ALA G 44 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR G 83 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N VAL G 65 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N VAL G 64 " --> pdb=" O ILE G 60 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ILE G 60 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY G 66 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N SER G 59 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 39 through 40 Processing sheet with id=AB6, first strand: chain 'H' and resid 81 through 83 removed outlier: 6.809A pdb=" N TYR H 43 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 63 through 64 removed outlier: 3.510A pdb=" N SER H 59 " --> pdb=" O LEU H 112 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 39 through 43 removed outlier: 3.531A pdb=" N ARG I 67 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL I 65 " --> pdb=" O GLU I 87 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU I 99 " --> pdb=" O LYS I 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 57 through 60 removed outlier: 3.994A pdb=" N GLY J 66 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE J 60 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL J 65 " --> pdb=" O GLU J 87 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR J 83 " --> pdb=" O ALA J 69 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA J 44 " --> pdb=" O VAL J 82 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ASP J 132 " --> pdb=" O THR J 41 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 98 through 100 Processing sheet with id=AC2, first strand: chain 'K' and resid 39 through 40 Processing sheet with id=AC3, first strand: chain 'K' and resid 43 through 45 removed outlier: 6.744A pdb=" N THR K 83 " --> pdb=" O ALA K 69 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N VAL K 64 " --> pdb=" O ILE K 60 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE K 60 " --> pdb=" O VAL K 64 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL K 58 " --> pdb=" O GLY K 66 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU K 114 " --> pdb=" O PRO K 57 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N SER K 59 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG K 102 " --> pdb=" O TYR K 111 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN K 115 " --> pdb=" O SER K 98 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER K 98 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU K 99 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 133 through 134 removed outlier: 8.787A pdb=" N ILE L 134 " --> pdb=" O THR L 41 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR L 43 " --> pdb=" O ILE L 134 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG L 67 " --> pdb=" O GLU L 85 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N VAL L 65 " --> pdb=" O GLU L 87 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU L 114 " --> pdb=" O PRO L 57 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N SER L 59 " --> pdb=" O LEU L 114 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU L 99 " --> pdb=" O LYS L 138 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5082 1.34 - 1.46: 2652 1.46 - 1.57: 8266 1.57 - 1.69: 10 1.69 - 1.81: 124 Bond restraints: 16134 Sorted by residual: bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.26e+01 bond pdb=" C4 ATP B 301 " pdb=" C5 ATP B 301 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C5 ATP B 301 " pdb=" C6 ATP B 301 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.48e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.476 -0.067 1.00e-02 1.00e+04 4.44e+01 bond pdb=" C5 ATP E 301 " pdb=" N7 ATP E 301 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.31e+01 ... (remaining 16129 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 21650 3.79 - 7.58: 267 7.58 - 11.37: 30 11.37 - 15.16: 1 15.16 - 18.95: 4 Bond angle restraints: 21952 Sorted by residual: angle pdb=" PB ATP E 301 " pdb=" O3B ATP E 301 " pdb=" PG ATP E 301 " ideal model delta sigma weight residual 139.87 120.92 18.95 1.00e+00 1.00e+00 3.59e+02 angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 120.94 18.93 1.00e+00 1.00e+00 3.58e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 119.25 17.58 1.00e+00 1.00e+00 3.09e+02 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 119.31 17.52 1.00e+00 1.00e+00 3.07e+02 angle pdb=" C5 ATP E 301 " pdb=" C4 ATP E 301 " pdb=" N3 ATP E 301 " ideal model delta sigma weight residual 126.80 118.28 8.52 1.00e+00 1.00e+00 7.26e+01 ... (remaining 21947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8532 17.94 - 35.88: 847 35.88 - 53.82: 226 53.82 - 71.77: 57 71.77 - 89.71: 12 Dihedral angle restraints: 9674 sinusoidal: 3720 harmonic: 5954 Sorted by residual: dihedral pdb=" CA THR J 77 " pdb=" C THR J 77 " pdb=" N TYR J 78 " pdb=" CA TYR J 78 " ideal model delta harmonic sigma weight residual -180.00 -153.22 -26.78 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA ASP G 95 " pdb=" C ASP G 95 " pdb=" N THR G 96 " pdb=" CA THR G 96 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA THR L 77 " pdb=" C THR L 77 " pdb=" N TYR L 78 " pdb=" CA TYR L 78 " ideal model delta harmonic sigma weight residual 180.00 154.90 25.10 0 5.00e+00 4.00e-02 2.52e+01 ... (remaining 9671 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2335 0.083 - 0.165: 298 0.165 - 0.248: 13 0.248 - 0.331: 3 0.331 - 0.414: 3 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CB ILE L 71 " pdb=" CA ILE L 71 " pdb=" CG1 ILE L 71 " pdb=" CG2 ILE L 71 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB ILE I 71 " pdb=" CA ILE I 71 " pdb=" CG1 ILE I 71 " pdb=" CG2 ILE I 71 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.30e+00 chirality pdb=" CB ILE H 71 " pdb=" CA ILE H 71 " pdb=" CG1 ILE H 71 " pdb=" CG2 ILE H 71 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 2649 not shown) Planarity restraints: 2764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 26 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO C 27 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 27 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 27 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 26 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO F 27 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO F 27 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 27 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 41 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO D 42 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 42 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 42 " -0.036 5.00e-02 4.00e+02 ... (remaining 2761 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 80 2.51 - 3.11: 10055 3.11 - 3.70: 22639 3.70 - 4.30: 31649 4.30 - 4.90: 53836 Nonbonded interactions: 118259 Sorted by model distance: nonbonded pdb=" O GLY B 259 " pdb=" O ASP B 260 " model vdw 1.910 3.040 nonbonded pdb=" N GLN E 230 " pdb=" OE1 GLN E 230 " model vdw 2.036 3.120 nonbonded pdb=" O HIS B 226 " pdb=" ND1 HIS B 226 " model vdw 2.129 3.120 nonbonded pdb=" OD1 ASP B 260 " pdb=" N TYR B 261 " model vdw 2.232 3.120 nonbonded pdb=" O TYR E 261 " pdb=" N ALA E 263 " model vdw 2.272 3.120 ... (remaining 118254 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = (chain 'G' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'H' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'I' selection = (chain 'J' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = (chain 'K' and ((resid 4 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 or (resid 12 through 30 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 152)) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.860 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 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 : 0.008 0.079 16134 Z= 0.361 Angle : 1.105 18.950 21952 Z= 0.658 Chirality : 0.056 0.414 2652 Planarity : 0.007 0.079 2764 Dihedral : 16.223 89.707 5850 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.75 % Favored : 89.01 % Rotamer: Outliers : 6.24 % Allowed : 10.34 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.21 (0.12), residues: 2056 helix: -4.84 (0.06), residues: 811 sheet: -3.29 (0.26), residues: 290 loop : -3.65 (0.16), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 233 TYR 0.036 0.002 TYR J 111 PHE 0.020 0.002 PHE B 254 TRP 0.012 0.002 TRP C 7 HIS 0.003 0.001 HIS E 122 Details of bonding type rmsd covalent geometry : bond 0.00780 (16134) covalent geometry : angle 1.10516 (21952) hydrogen bonds : bond 0.31808 ( 522) hydrogen bonds : angle 11.34493 ( 1482) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4112 Ramachandran restraints generated. 2056 Oldfield, 0 Emsley, 2056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 387 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 9 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6984 (tp) REVERT: A 72 LEU cc_start: 0.8444 (mm) cc_final: 0.8040 (mt) REVERT: A 111 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8629 (tmm160) REVERT: A 122 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8318 (tp) REVERT: A 203 LEU cc_start: 0.8732 (mt) cc_final: 0.8437 (mt) REVERT: B 130 GLU cc_start: 0.8649 (mm-30) cc_final: 0.7888 (tt0) REVERT: B 176 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8417 (p0) REVERT: B 222 LYS cc_start: 0.8345 (pttt) cc_final: 0.7548 (ptmm) REVERT: B 242 GLN cc_start: 0.6892 (tm-30) cc_final: 0.6486 (tm-30) REVERT: E 139 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8325 (mmtp) REVERT: E 207 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: E 222 LYS cc_start: 0.8292 (pttt) cc_final: 0.7908 (ptpp) REVERT: D 38 ARG cc_start: 0.7016 (OUTLIER) cc_final: 0.6491 (mmt180) REVERT: D 129 LEU cc_start: 0.9296 (mt) cc_final: 0.9080 (mt) REVERT: D 134 MET cc_start: 0.8799 (tpt) cc_final: 0.8585 (tpt) REVERT: C 32 ARG cc_start: 0.6746 (ptt90) cc_final: 0.6545 (ptt-90) REVERT: C 81 VAL cc_start: 0.8849 (OUTLIER) cc_final: 0.8649 (m) REVERT: F 83 THR cc_start: 0.8914 (t) cc_final: 0.8714 (m) REVERT: G 74 ASP cc_start: 0.7947 (t0) cc_final: 0.7712 (t0) REVERT: G 134 ILE cc_start: 0.8664 (mt) cc_final: 0.8450 (mp) REVERT: H 102 ARG cc_start: 0.8339 (mtt180) cc_final: 0.7910 (mtm-85) REVERT: J 30 ASN cc_start: 0.6046 (OUTLIER) cc_final: 0.5539 (m-40) REVERT: J 85 GLU cc_start: 0.8111 (tt0) cc_final: 0.7564 (tt0) REVERT: K 48 ASN cc_start: 0.8274 (m110) cc_final: 0.8013 (t0) outliers start: 105 outliers final: 21 residues processed: 457 average time/residue: 0.1333 time to fit residues: 86.6183 Evaluate side-chains 330 residues out of total 1724 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 301 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 LEU Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain B residue 28 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 176 ASP Chi-restraints excluded: chain B residue 226 HIS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 262 HIS Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 207 GLU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 230 GLN Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain D residue 243 SER Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain F residue 10 THR Chi-restraints excluded: chain F residue 13 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain J residue 30 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6453 > 50: distance: 40 - 44: 14.473 distance: 44 - 45: 23.840 distance: 45 - 46: 20.922 distance: 45 - 48: 18.143 distance: 46 - 47: 13.360 distance: 46 - 52: 16.914 distance: 48 - 49: 11.001 distance: 49 - 50: 7.089 distance: 49 - 51: 3.909 distance: 52 - 53: 21.460 distance: 53 - 54: 19.184 distance: 53 - 56: 18.051 distance: 54 - 55: 41.117 distance: 54 - 60: 13.864 distance: 56 - 57: 26.070 distance: 56 - 58: 30.594 distance: 57 - 59: 15.178 distance: 60 - 61: 14.605 distance: 61 - 62: 36.910 distance: 62 - 63: 58.645 distance: 62 - 64: 34.354 distance: 64 - 65: 43.306 distance: 65 - 66: 31.780 distance: 66 - 67: 31.977 distance: 66 - 68: 42.815 distance: 68 - 69: 28.312 distance: 69 - 70: 13.941 distance: 69 - 72: 6.722 distance: 70 - 71: 5.543 distance: 70 - 76: 19.256 distance: 72 - 73: 13.134 distance: 73 - 74: 9.433 distance: 73 - 75: 10.008 distance: 76 - 77: 9.226 distance: 77 - 78: 22.311 distance: 77 - 80: 14.104 distance: 78 - 79: 11.483 distance: 78 - 85: 36.858 distance: 80 - 81: 18.419 distance: 81 - 82: 8.320 distance: 82 - 83: 3.480 distance: 85 - 86: 14.112 distance: 86 - 87: 17.053 distance: 86 - 89: 23.065 distance: 87 - 88: 5.759 distance: 87 - 90: 7.367 distance: 90 - 91: 16.709 distance: 91 - 92: 19.779 distance: 91 - 94: 15.342 distance: 92 - 93: 12.325 distance: 92 - 101: 37.709 distance: 94 - 95: 23.544 distance: 95 - 96: 8.697 distance: 96 - 97: 13.293 distance: 97 - 98: 5.743 distance: 98 - 99: 5.290 distance: 98 - 100: 3.276 distance: 101 - 102: 35.733 distance: 102 - 103: 13.839 distance: 102 - 105: 40.503 distance: 103 - 104: 20.002 distance: 103 - 107: 10.354 distance: 105 - 106: 24.067 distance: 107 - 108: 5.354 distance: 107 - 113: 13.849 distance: 108 - 109: 15.451 distance: 108 - 111: 18.196 distance: 109 - 110: 8.531 distance: 109 - 114: 12.097 distance: 111 - 112: 17.008 distance: 112 - 113: 17.560