Starting phenix.real_space_refine on Sun Jul 21 20:45:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgn_30358/07_2024/7cgn_30358.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgn_30358/07_2024/7cgn_30358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgn_30358/07_2024/7cgn_30358.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgn_30358/07_2024/7cgn_30358.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgn_30358/07_2024/7cgn_30358.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cgn_30358/07_2024/7cgn_30358.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 6 5.49 5 S 68 5.16 5 C 10164 2.51 5 N 2666 2.21 5 O 2950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ARG 196": "NH1" <-> "NH2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 112": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ARG 157": "NH1" <-> "NH2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B ASP 176": "OD1" <-> "OD2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "D ARG 141": "NH1" <-> "NH2" Residue "D ARG 196": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E ASP 176": "OD1" <-> "OD2" Residue "E PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "H ARG 55": "NH1" <-> "NH2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H GLU 144": "OE1" <-> "OE2" Residue "I ARG 55": "NH1" <-> "NH2" Residue "I GLU 119": "OE1" <-> "OE2" Residue "I GLU 144": "OE1" <-> "OE2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J GLU 144": "OE1" <-> "OE2" Residue "K ARG 55": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L ASP 70": "OD1" <-> "OD2" Residue "L GLU 119": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15854 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: "C" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} 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: "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: "F" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 724 Classifications: {'peptide': 94} 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: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} 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: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} 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: 8.18, per 1000 atoms: 0.52 Number of scatterers: 15854 At special positions: 0 Unit cell: (104.352, 116.309, 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 2950 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 - 3.50 Amino acid : False - 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: 6.73 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 64 helices and 20 sheets defined 42.9% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 5 through 31 removed outlier: 3.752A pdb=" N LEU A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS A 12 " --> pdb=" O SER A 8 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 19 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 52 removed outlier: 3.710A pdb=" N VAL A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG A 46 " --> pdb=" O PRO A 42 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 3.804A pdb=" N ILE A 59 " --> pdb=" O SER A 55 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 87 through 96 removed outlier: 3.822A pdb=" N ALA A 92 " --> pdb=" O GLY A 88 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 126 removed outlier: 3.705A pdb=" N VAL A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR A 117 " --> pdb=" O GLY A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 133 removed outlier: 3.533A 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 153 removed outlier: 3.588A pdb=" N VAL A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 174 removed outlier: 4.001A pdb=" N LEU A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 191 removed outlier: 3.686A pdb=" N TRP A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 189 " --> pdb=" O PHE A 185 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 221 removed outlier: 4.022A pdb=" N LEU A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 258 removed outlier: 4.136A pdb=" N SER A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.769A pdb=" N LEU B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 removed outlier: 3.863A pdb=" N ALA B 74 " --> pdb=" O ASN B 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET B 75 " --> pdb=" O ILE B 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 75' Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 101 through 107 Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 117 through 132 removed outlier: 3.878A pdb=" N LYS B 128 " --> pdb=" O THR B 124 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 132 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.539A pdb=" N ARG B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG B 152 " --> pdb=" O GLY B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 193 removed outlier: 3.520A pdb=" N LYS B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU B 189 " --> pdb=" O LYS B 185 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 Processing helix chain 'B' and resid 237 through 246 Processing helix chain 'C' and resid 25 through 31 Processing helix chain 'C' and resid 51 through 64 Processing helix chain 'C' and resid 80 through 88 removed outlier: 3.669A pdb=" N LYS C 86 " --> pdb=" O TYR C 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 31 removed outlier: 3.752A pdb=" N LEU D 9 " --> pdb=" O ALA D 5 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS D 12 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU D 17 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR D 19 " --> pdb=" O LYS D 15 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 52 removed outlier: 3.710A pdb=" N VAL D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG D 46 " --> pdb=" O PRO D 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR D 49 " --> pdb=" O VAL D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 3.803A pdb=" N ILE D 59 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N PHE D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU D 76 " --> pdb=" O LEU D 72 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 87 through 96 removed outlier: 3.822A pdb=" N ALA D 92 " --> pdb=" O GLY D 88 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU D 93 " --> pdb=" O MET D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 126 removed outlier: 3.705A pdb=" N VAL D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 104 " --> pdb=" O GLY D 100 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR D 117 " --> pdb=" O GLY D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 133 removed outlier: 3.533A 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 153 removed outlier: 3.589A pdb=" N VAL D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 174 removed outlier: 4.000A pdb=" N LEU D 157 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 164 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY D 174 " --> pdb=" O GLY D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.687A pdb=" N TRP D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA D 188 " --> pdb=" O PHE D 184 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET D 189 " --> pdb=" O PHE D 185 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN D 191 " --> pdb=" O SER D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 221 removed outlier: 4.021A pdb=" N LEU D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL D 208 " --> pdb=" O ILE D 204 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 212 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TRP D 215 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 258 removed outlier: 4.137A pdb=" N SER D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL D 240 " --> pdb=" O THR D 236 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 244 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU D 247 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE D 258 " --> pdb=" O THR D 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 removed outlier: 3.769A pdb=" N LEU E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 75 removed outlier: 3.864A pdb=" N ALA E 74 " --> pdb=" O ASN E 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET E 75 " --> pdb=" O ILE E 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 75' Processing helix chain 'E' and resid 76 through 84 Processing helix chain 'E' and resid 101 through 107 Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'E' and resid 117 through 132 removed outlier: 3.878A pdb=" N LYS E 128 " --> pdb=" O THR E 124 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU E 130 " --> pdb=" O MET E 126 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL E 132 " --> pdb=" O LYS E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 159 removed outlier: 3.540A pdb=" N ARG E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG E 152 " --> pdb=" O GLY E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 3.520A pdb=" N LYS E 185 " --> pdb=" O GLY E 181 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 189 " --> pdb=" O LYS E 185 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN E 191 " --> pdb=" O ILE E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 237 through 246 Processing helix chain 'F' and resid 25 through 31 Processing helix chain 'F' and resid 51 through 64 Processing helix chain 'F' and resid 80 through 88 removed outlier: 3.669A pdb=" N LYS F 86 " --> pdb=" O TYR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 26 removed outlier: 3.540A pdb=" N TRP G 9 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY G 11 " --> pdb=" O GLU G 7 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N CYS G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 150 Processing helix chain 'H' and resid 9 through 28 removed outlier: 3.985A pdb=" N PHE H 13 " --> pdb=" O TRP H 9 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS H 25 " --> pdb=" O ALA H 21 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS H 27 " --> pdb=" O PHE H 23 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 152 removed outlier: 3.759A pdb=" N PHE H 150 " --> pdb=" O LEU H 146 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU H 151 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR H 152 " --> pdb=" O GLY H 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 28 removed outlier: 4.028A pdb=" N TRP I 9 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL I 10 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE I 13 " --> pdb=" O TRP I 9 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 152 removed outlier: 3.515A pdb=" N PHE I 150 " --> pdb=" O LEU I 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 29 removed outlier: 3.702A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 removed outlier: 3.515A pdb=" N PHE J 150 " --> pdb=" O LEU J 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 29 removed outlier: 3.993A pdb=" N ALA K 28 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA K 29 " --> pdb=" O CYS K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 152 removed outlier: 4.568A pdb=" N LEU K 146 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 28 Processing helix chain 'L' and resid 143 through 151 removed outlier: 3.565A pdb=" N PHE L 150 " --> pdb=" O LEU L 146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 32 removed outlier: 6.033A pdb=" N ILE B 27 " --> pdb=" O ASP B 13 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP B 13 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU B 29 " --> pdb=" O MET B 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.721A pdb=" N SER B 88 " --> pdb=" O MET B 167 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASP B 169 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU B 90 " --> pdb=" O ASP B 169 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 37 " --> pdb=" O CYS B 198 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ILE B 36 " --> pdb=" O HIS B 214 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N TRP B 216 " --> pdb=" O ILE B 36 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA B 38 " --> pdb=" O TRP B 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AA4, first strand: chain 'E' and resid 27 through 32 removed outlier: 6.033A pdb=" N ILE E 27 " --> pdb=" O ASP E 13 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ASP E 13 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU E 29 " --> pdb=" O MET E 11 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 87 through 90 removed outlier: 6.720A pdb=" N SER E 88 " --> pdb=" O MET E 167 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ASP E 169 " --> pdb=" O SER E 88 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU E 90 " --> pdb=" O ASP E 169 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 37 " --> pdb=" O CYS E 198 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE E 36 " --> pdb=" O HIS E 214 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N TRP E 216 " --> pdb=" O ILE E 36 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA E 38 " --> pdb=" O TRP E 216 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 41 through 42 Processing sheet with id=AA7, first strand: chain 'G' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'G' and resid 97 through 98 removed outlier: 6.815A pdb=" N VAL G 58 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 10.119A pdb=" N VAL G 65 " --> pdb=" O GLU G 87 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU G 87 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG G 67 " --> pdb=" O GLU G 85 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU G 85 " --> pdb=" O ARG G 67 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU G 42 " --> pdb=" O LEU G 84 " (cutoff:3.500A) removed outlier: 9.455A pdb=" N ILE G 134 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYR G 43 " --> pdb=" O ILE G 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 81 through 87 removed outlier: 8.825A pdb=" N ILE H 134 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR H 43 " --> pdb=" O ILE H 134 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 63 through 67 removed outlier: 6.864A pdb=" N VAL H 58 " --> pdb=" O VAL H 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 39 through 40 Processing sheet with id=AB3, first strand: chain 'I' and resid 63 through 68 removed outlier: 3.686A pdb=" N VAL I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ARG I 67 " --> pdb=" O SER I 56 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER I 56 " --> pdb=" O ARG I 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 81 through 87 removed outlier: 3.634A pdb=" N LEU J 42 " --> pdb=" O LEU J 84 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ILE J 134 " --> pdb=" O THR J 41 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N TYR J 43 " --> pdb=" O ILE J 134 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 63 through 67 removed outlier: 3.751A pdb=" N VAL J 63 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL J 58 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU J 114 " --> pdb=" O PRO J 57 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N SER J 59 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL J 116 " --> pdb=" O SER J 59 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 39 through 40 Processing sheet with id=AB7, first strand: chain 'K' and resid 81 through 83 removed outlier: 7.754A pdb=" N TYR K 43 " --> pdb=" O ILE K 134 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 63 through 68 removed outlier: 6.382A pdb=" N VAL K 58 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG K 67 " --> pdb=" O SER K 56 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N SER K 56 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 63 through 68 removed outlier: 6.382A pdb=" N VAL K 58 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ARG K 67 " --> pdb=" O SER K 56 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N SER K 56 " --> pdb=" O ARG K 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 39 through 40 Processing sheet with id=AC2, first strand: chain 'L' and resid 63 through 67 removed outlier: 6.732A pdb=" N VAL L 58 " --> pdb=" O VAL L 65 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1782 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: 4.67 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5142 1.35 - 1.47: 3629 1.47 - 1.60: 7227 1.60 - 1.72: 10 1.72 - 1.84: 124 Bond restraints: 16132 Sorted by residual: bond pdb=" C4 ATP E 301 " pdb=" C5 ATP E 301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 bond pdb=" C4 ATP B 301 " pdb=" C5 ATP B 301 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.86e+01 bond pdb=" C5 ATP E 301 " pdb=" C6 ATP E 301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.34e+01 bond pdb=" C5 ATP B 301 " pdb=" C6 ATP B 301 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.33e+01 bond pdb=" C8 ATP E 301 " pdb=" N7 ATP E 301 " ideal model delta sigma weight residual 1.310 1.358 -0.048 1.00e-02 1.00e+04 2.30e+01 ... (remaining 16127 not shown) Histogram of bond angle deviations from ideal: 98.84 - 106.30: 454 106.30 - 113.75: 9344 113.75 - 121.21: 7825 121.21 - 128.66: 4221 128.66 - 136.12: 104 Bond angle restraints: 21948 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 139.87 120.50 19.37 1.00e+00 1.00e+00 3.75e+02 angle pdb=" PB ATP B 301 " pdb=" O3B ATP B 301 " pdb=" PG ATP B 301 " ideal model delta sigma weight residual 139.87 120.56 19.31 1.00e+00 1.00e+00 3.73e+02 angle pdb=" PA ATP E 301 " pdb=" O3A ATP E 301 " pdb=" PB ATP E 301 " ideal model delta sigma weight residual 136.83 120.47 16.36 1.00e+00 1.00e+00 2.68e+02 angle pdb=" PA ATP B 301 " pdb=" O3A ATP B 301 " pdb=" PB ATP B 301 " ideal model delta sigma weight residual 136.83 120.51 16.32 1.00e+00 1.00e+00 2.66e+02 angle pdb=" C5 ATP E 301 " pdb=" C4 ATP E 301 " pdb=" N3 ATP E 301 " ideal model delta sigma weight residual 126.80 118.64 8.16 1.00e+00 1.00e+00 6.67e+01 ... (remaining 21943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 8421 17.12 - 34.23: 867 34.23 - 51.35: 267 51.35 - 68.47: 94 68.47 - 85.59: 23 Dihedral angle restraints: 9672 sinusoidal: 3718 harmonic: 5954 Sorted by residual: dihedral pdb=" CA GLN J 135 " pdb=" C GLN J 135 " pdb=" N ASP J 136 " pdb=" CA ASP J 136 " ideal model delta harmonic sigma weight residual 180.00 152.81 27.19 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ALA K 140 " pdb=" C ALA K 140 " pdb=" N MET K 141 " pdb=" CA MET K 141 " ideal model delta harmonic sigma weight residual 180.00 155.54 24.46 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA VAL J 142 " pdb=" C VAL J 142 " pdb=" N LEU J 143 " pdb=" CA LEU J 143 " ideal model delta harmonic sigma weight residual -180.00 -155.55 -24.45 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 9669 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2114 0.064 - 0.129: 443 0.129 - 0.193: 76 0.193 - 0.257: 15 0.257 - 0.321: 4 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CB ILE B 223 " pdb=" CA ILE B 223 " pdb=" CG1 ILE B 223 " pdb=" CG2 ILE B 223 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE E 223 " pdb=" CA ILE E 223 " pdb=" CG1 ILE E 223 " pdb=" CG2 ILE E 223 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE J 60 " pdb=" CA ILE J 60 " pdb=" CG1 ILE J 60 " pdb=" CG2 ILE J 60 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 2649 not shown) Planarity restraints: 2762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 16 " -0.024 2.00e-02 2.50e+03 2.39e-02 9.99e+00 pdb=" CG PHE E 16 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE E 16 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE E 16 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE E 16 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE E 16 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE E 16 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 16 " 0.024 2.00e-02 2.50e+03 2.38e-02 9.94e+00 pdb=" CG PHE B 16 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE B 16 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE B 16 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 16 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 16 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 16 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 41 " -0.049 5.00e-02 4.00e+02 7.46e-02 8.89e+00 pdb=" N PRO B 42 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 42 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 42 " -0.040 5.00e-02 4.00e+02 ... (remaining 2759 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2668 2.76 - 3.30: 14898 3.30 - 3.83: 26061 3.83 - 4.37: 28802 4.37 - 4.90: 48214 Nonbonded interactions: 120643 Sorted by model distance: nonbonded pdb=" O ALA K 69 " pdb=" N ILE K 71 " model vdw 2.225 2.520 nonbonded pdb=" O GLY A 110 " pdb=" OG SER A 114 " model vdw 2.230 2.440 nonbonded pdb=" O GLY D 110 " pdb=" OG SER D 114 " model vdw 2.231 2.440 nonbonded pdb=" O PRO B 42 " pdb=" CG ASP E 176 " model vdw 2.242 3.270 nonbonded pdb=" OG SER I 100 " pdb=" O ALA I 113 " model vdw 2.252 2.440 ... (remaining 120638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.640 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 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 : 0.006 0.083 16132 Z= 0.375 Angle : 1.118 19.367 21948 Z= 0.678 Chirality : 0.057 0.321 2652 Planarity : 0.007 0.075 2762 Dihedral : 16.920 85.586 5848 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.44 % Favored : 89.83 % Rotamer: Outliers : 6.36 % Allowed : 9.75 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.60 (0.13), residues: 2056 helix: -4.23 (0.08), residues: 801 sheet: -3.05 (0.28), residues: 254 loop : -3.41 (0.16), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 216 HIS 0.006 0.001 HIS K 92 PHE 0.054 0.002 PHE B 16 TYR 0.020 0.002 TYR H 40 ARG 0.006 0.001 ARG E 18 *********************** 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 617 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 510 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 TYR cc_start: 0.7525 (m-80) cc_final: 0.7273 (m-80) REVERT: A 189 MET cc_start: 0.6996 (ttm) cc_final: 0.6657 (ttm) REVERT: A 201 ASN cc_start: 0.8626 (t0) cc_final: 0.8268 (t0) REVERT: A 251 PHE cc_start: 0.8406 (t80) cc_final: 0.7979 (t80) REVERT: B 10 ASP cc_start: 0.7381 (t0) cc_final: 0.6881 (t0) REVERT: B 20 ASN cc_start: 0.6980 (OUTLIER) cc_final: 0.6747 (p0) REVERT: B 89 MET cc_start: 0.7196 (mtp) cc_final: 0.6968 (mtp) REVERT: B 100 MET cc_start: 0.7869 (mtt) cc_final: 0.7148 (mtt) REVERT: B 172 PHE cc_start: 0.8292 (m-80) cc_final: 0.7811 (m-80) REVERT: B 224 VAL cc_start: 0.8201 (OUTLIER) cc_final: 0.7792 (p) REVERT: C 59 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.8884 (tt) REVERT: C 74 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7798 (mm) REVERT: C 80 LYS cc_start: 0.9057 (mmtp) cc_final: 0.8828 (mmmt) REVERT: D 14 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8827 (tp) REVERT: D 135 MET cc_start: 0.8936 (mmt) cc_final: 0.8686 (mmp) REVERT: D 243 SER cc_start: 0.9724 (OUTLIER) cc_final: 0.9288 (t) REVERT: E 28 SER cc_start: 0.7412 (OUTLIER) cc_final: 0.6859 (t) REVERT: E 29 LEU cc_start: 0.8551 (pp) cc_final: 0.8164 (pp) REVERT: E 85 LYS cc_start: 0.8750 (mppt) cc_final: 0.8261 (mtpt) REVERT: E 126 MET cc_start: 0.9343 (tpp) cc_final: 0.8889 (tpp) REVERT: E 167 MET cc_start: 0.6955 (mtt) cc_final: 0.5822 (mtt) REVERT: E 202 SER cc_start: 0.8747 (OUTLIER) cc_final: 0.8523 (p) REVERT: F 74 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7069 (tp) REVERT: F 79 ASP cc_start: 0.7664 (t0) cc_final: 0.7448 (t0) REVERT: F 86 LYS cc_start: 0.8700 (pttt) cc_final: 0.8336 (tmtt) REVERT: G 12 ILE cc_start: 0.8905 (mt) cc_final: 0.8276 (tp) REVERT: G 40 TYR cc_start: 0.3456 (p90) cc_final: 0.3077 (p90) REVERT: G 48 ASN cc_start: 0.4710 (t0) cc_final: 0.4157 (p0) REVERT: G 81 ARG cc_start: 0.7323 (tmm160) cc_final: 0.6836 (ttp80) REVERT: G 89 ARG cc_start: 0.7487 (ptt-90) cc_final: 0.7143 (mtm-85) REVERT: G 145 ASP cc_start: 0.8790 (t0) cc_final: 0.8133 (p0) REVERT: H 6 ASN cc_start: 0.8646 (p0) cc_final: 0.8217 (p0) REVERT: H 90 TYR cc_start: 0.4957 (m-80) cc_final: 0.4715 (m-10) REVERT: H 130 ASP cc_start: 0.8383 (p0) cc_final: 0.7818 (p0) REVERT: H 135 GLN cc_start: 0.6918 (mt0) cc_final: 0.6668 (mp-120) REVERT: I 52 LEU cc_start: 0.3370 (tt) cc_final: 0.2824 (tt) REVERT: I 78 TYR cc_start: 0.6560 (m-10) cc_final: 0.4693 (p90) REVERT: I 88 GLN cc_start: 0.6454 (mt0) cc_final: 0.5430 (tm-30) REVERT: J 53 LYS cc_start: 0.7304 (mptt) cc_final: 0.6973 (ptpt) REVERT: K 88 GLN cc_start: 0.6898 (tp-100) cc_final: 0.6549 (pp30) REVERT: K 109 GLU cc_start: 0.7961 (mp0) cc_final: 0.7685 (mp0) outliers start: 107 outliers final: 15 residues processed: 569 average time/residue: 0.3003 time to fit residues: 242.7024 Evaluate side-chains 335 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 311 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 10.0000 chunk 154 optimal weight: 0.0070 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 104 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 159 optimal weight: 0.5980 chunk 61 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 119 optimal weight: 6.9990 chunk 185 optimal weight: 40.0000 overall best weight: 2.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN A 73 GLN A 220 ASN A 241 HIS B 105 ASN B 122 HIS B 191 ASN B 226 HIS C 60 HIS C 68 GLN C 75 GLN D 11 HIS D 29 ASN D 220 ASN E 26 ASN E 122 HIS E 191 ASN E 226 HIS E 262 HIS F 89 ASN H 88 GLN I 91 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16132 Z= 0.224 Angle : 0.735 9.708 21948 Z= 0.378 Chirality : 0.046 0.258 2652 Planarity : 0.006 0.058 2762 Dihedral : 7.932 87.953 2296 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.71 % Favored : 90.86 % Rotamer: Outliers : 0.30 % Allowed : 6.30 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.16), residues: 2056 helix: -1.64 (0.15), residues: 836 sheet: -2.49 (0.30), residues: 275 loop : -3.29 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 216 HIS 0.006 0.001 HIS D 11 PHE 0.022 0.002 PHE H 23 TYR 0.014 0.001 TYR I 40 ARG 0.007 0.001 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 2 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 397 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 392 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8351 (pm20) cc_final: 0.7759 (pm20) REVERT: A 153 ILE cc_start: 0.9318 (mm) cc_final: 0.9055 (mt) REVERT: B 10 ASP cc_start: 0.7566 (t0) cc_final: 0.7260 (t0) REVERT: B 89 MET cc_start: 0.7409 (mtp) cc_final: 0.6919 (mtp) REVERT: B 91 PHE cc_start: 0.8261 (m-80) cc_final: 0.8038 (m-80) REVERT: B 172 PHE cc_start: 0.8284 (m-80) cc_final: 0.8011 (m-80) REVERT: C 59 LEU cc_start: 0.8922 (tp) cc_final: 0.8410 (tt) REVERT: C 63 ASP cc_start: 0.8009 (m-30) cc_final: 0.7603 (m-30) REVERT: C 68 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6398 (tm-30) REVERT: D 135 MET cc_start: 0.8875 (mmt) cc_final: 0.8621 (mmp) REVERT: E 11 MET cc_start: 0.8262 (ptp) cc_final: 0.7938 (ptp) REVERT: E 67 PHE cc_start: 0.8283 (t80) cc_final: 0.8053 (t80) REVERT: E 85 LYS cc_start: 0.8688 (mppt) cc_final: 0.8442 (mtpt) REVERT: E 89 MET cc_start: 0.8490 (mmt) cc_final: 0.8236 (mmm) REVERT: E 126 MET cc_start: 0.9169 (tpp) cc_final: 0.8944 (tpp) REVERT: F 26 LEU cc_start: 0.7612 (pt) cc_final: 0.7375 (tp) REVERT: F 86 LYS cc_start: 0.8748 (pttt) cc_final: 0.8476 (tmtt) REVERT: F 93 ASP cc_start: 0.7183 (p0) cc_final: 0.6580 (t70) REVERT: G 48 ASN cc_start: 0.4373 (t0) cc_final: 0.4062 (p0) REVERT: G 72 THR cc_start: 0.4917 (t) cc_final: 0.4105 (p) REVERT: G 81 ARG cc_start: 0.7263 (tmm160) cc_final: 0.6866 (ttp80) REVERT: G 103 THR cc_start: 0.6254 (m) cc_final: 0.5619 (t) REVERT: G 145 ASP cc_start: 0.8548 (t0) cc_final: 0.7760 (p0) REVERT: H 6 ASN cc_start: 0.8622 (p0) cc_final: 0.8418 (p0) REVERT: J 52 LEU cc_start: 0.5701 (tt) cc_final: 0.5205 (tt) REVERT: J 53 LYS cc_start: 0.7317 (mptt) cc_final: 0.6970 (ptpt) REVERT: K 88 GLN cc_start: 0.6938 (tp-100) cc_final: 0.6408 (pp30) REVERT: K 109 GLU cc_start: 0.7680 (mp0) cc_final: 0.7051 (mp0) REVERT: L 81 ARG cc_start: 0.6839 (ttp80) cc_final: 0.6340 (ttp80) outliers start: 5 outliers final: 0 residues processed: 396 average time/residue: 0.2913 time to fit residues: 169.6851 Evaluate side-chains 283 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 282 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 126 optimal weight: 30.0000 chunk 51 optimal weight: 9.9990 chunk 185 optimal weight: 0.8980 chunk 200 optimal weight: 30.0000 chunk 165 optimal weight: 5.9990 chunk 184 optimal weight: 30.0000 chunk 63 optimal weight: 0.0370 chunk 148 optimal weight: 6.9990 overall best weight: 2.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN B 214 HIS C 9 GLN ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 ASN E 214 HIS F 9 GLN F 68 GLN G 88 GLN H 135 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16132 Z= 0.207 Angle : 0.676 8.827 21948 Z= 0.346 Chirality : 0.045 0.223 2652 Planarity : 0.005 0.104 2762 Dihedral : 7.421 88.494 2296 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.29 % Allowed : 9.19 % Favored : 90.52 % Rotamer: Outliers : 0.24 % Allowed : 5.53 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.17), residues: 2056 helix: -0.41 (0.18), residues: 831 sheet: -2.23 (0.31), residues: 257 loop : -3.12 (0.18), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 215 HIS 0.005 0.001 HIS B 262 PHE 0.037 0.002 PHE E 16 TYR 0.018 0.002 TYR B 261 ARG 0.009 0.001 ARG J 81 *********************** REFINEMENT MACRO_CYCLE 3 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 392 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 388 time to evaluate : 1.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ILE cc_start: 0.9398 (mm) cc_final: 0.9119 (mt) REVERT: B 10 ASP cc_start: 0.7389 (t0) cc_final: 0.7154 (t0) REVERT: B 89 MET cc_start: 0.7806 (mtp) cc_final: 0.7218 (mtp) REVERT: B 91 PHE cc_start: 0.8075 (m-80) cc_final: 0.7850 (m-80) REVERT: D 135 MET cc_start: 0.8914 (mmt) cc_final: 0.8574 (mmp) REVERT: E 11 MET cc_start: 0.8365 (ptp) cc_final: 0.8070 (ptp) REVERT: E 170 GLN cc_start: 0.8888 (tp-100) cc_final: 0.8431 (tm-30) REVERT: E 237 ASP cc_start: 0.7749 (t70) cc_final: 0.7531 (t0) REVERT: F 26 LEU cc_start: 0.7616 (pt) cc_final: 0.7338 (tp) REVERT: F 86 LYS cc_start: 0.8824 (pttt) cc_final: 0.8508 (tmtt) REVERT: F 93 ASP cc_start: 0.7341 (p0) cc_final: 0.6679 (t70) REVERT: G 48 ASN cc_start: 0.4109 (t0) cc_final: 0.3738 (p0) REVERT: G 72 THR cc_start: 0.4965 (t) cc_final: 0.4092 (p) REVERT: G 81 ARG cc_start: 0.7335 (tmm160) cc_final: 0.6800 (ttp80) REVERT: G 103 THR cc_start: 0.6170 (m) cc_final: 0.5581 (t) REVERT: G 145 ASP cc_start: 0.8479 (t0) cc_final: 0.7668 (p0) REVERT: H 6 ASN cc_start: 0.8622 (p0) cc_final: 0.8177 (p0) REVERT: H 147 ILE cc_start: 0.8184 (pt) cc_final: 0.7961 (pt) REVERT: H 152 TYR cc_start: 0.7649 (m-80) cc_final: 0.7441 (m-80) REVERT: I 55 ARG cc_start: 0.5389 (tpp80) cc_final: 0.5155 (mmm160) REVERT: J 53 LYS cc_start: 0.7325 (mptt) cc_final: 0.6991 (ptpt) REVERT: K 88 GLN cc_start: 0.7046 (tp-100) cc_final: 0.6535 (pp30) REVERT: K 109 GLU cc_start: 0.7458 (mp0) cc_final: 0.6827 (mp0) REVERT: L 81 ARG cc_start: 0.6684 (ttp80) cc_final: 0.6137 (ttp80) outliers start: 4 outliers final: 1 residues processed: 392 average time/residue: 0.2652 time to fit residues: 152.5867 Evaluate side-chains 291 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 290 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 30.0000 chunk 139 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 124 optimal weight: 30.0000 chunk 186 optimal weight: 40.0000 chunk 197 optimal weight: 20.0000 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN B 226 HIS C 60 HIS C 89 ASN I 91 ASN J 92 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16132 Z= 0.303 Angle : 0.761 8.460 21948 Z= 0.386 Chirality : 0.048 0.181 2652 Planarity : 0.005 0.055 2762 Dihedral : 7.308 81.840 2296 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.36 % Favored : 89.40 % Rotamer: Outliers : 0.06 % Allowed : 5.59 % Favored : 94.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.18), residues: 2056 helix: -0.21 (0.18), residues: 844 sheet: -2.07 (0.32), residues: 242 loop : -2.96 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 216 HIS 0.005 0.001 HIS B 122 PHE 0.038 0.002 PHE E 16 TYR 0.027 0.002 TYR B 261 ARG 0.008 0.001 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 4 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 341 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 340 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLU cc_start: 0.8269 (pm20) cc_final: 0.7749 (pm20) REVERT: B 75 MET cc_start: 0.7552 (ptp) cc_final: 0.7176 (ptp) REVERT: B 89 MET cc_start: 0.7897 (mtp) cc_final: 0.7635 (mtp) REVERT: B 100 MET cc_start: 0.7963 (mtt) cc_final: 0.7702 (mtm) REVERT: C 59 LEU cc_start: 0.9225 (mm) cc_final: 0.8884 (mm) REVERT: D 84 GLU cc_start: 0.8283 (mm-30) cc_final: 0.8044 (tp30) REVERT: E 126 MET cc_start: 0.9151 (tpp) cc_final: 0.8857 (tpp) REVERT: F 86 LYS cc_start: 0.8876 (pttt) cc_final: 0.8571 (tmtt) REVERT: F 93 ASP cc_start: 0.7516 (p0) cc_final: 0.6794 (t70) REVERT: G 72 THR cc_start: 0.5680 (t) cc_final: 0.4668 (p) REVERT: G 81 ARG cc_start: 0.7501 (tmm160) cc_final: 0.6917 (ttp80) REVERT: G 145 ASP cc_start: 0.8618 (t0) cc_final: 0.7721 (p0) REVERT: H 90 TYR cc_start: 0.4149 (m-10) cc_final: 0.3616 (m-10) REVERT: I 129 LYS cc_start: 0.7817 (pttt) cc_final: 0.7130 (mtmt) REVERT: J 53 LYS cc_start: 0.7390 (mptt) cc_final: 0.7025 (ptpt) REVERT: K 88 GLN cc_start: 0.6755 (tp-100) cc_final: 0.6513 (pp30) REVERT: K 109 GLU cc_start: 0.7180 (mp0) cc_final: 0.6499 (mp0) outliers start: 1 outliers final: 0 residues processed: 341 average time/residue: 0.2735 time to fit residues: 136.6640 Evaluate side-chains 257 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 168 optimal weight: 20.0000 chunk 136 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 ASN D 40 HIS E 214 HIS J 91 ASN L 110 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16132 Z= 0.243 Angle : 0.695 8.574 21948 Z= 0.350 Chirality : 0.046 0.178 2652 Planarity : 0.005 0.055 2762 Dihedral : 7.268 80.243 2296 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.58 % Favored : 90.18 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.18), residues: 2056 helix: 0.18 (0.18), residues: 839 sheet: -2.05 (0.31), residues: 265 loop : -2.87 (0.19), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 216 HIS 0.004 0.001 HIS D 40 PHE 0.019 0.002 PHE B 16 TYR 0.025 0.002 TYR A 222 ARG 0.009 0.001 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 5 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 350 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 350 time to evaluate : 1.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7743 (pm20) cc_final: 0.7361 (pm20) REVERT: A 194 ASP cc_start: 0.7363 (p0) cc_final: 0.6692 (p0) REVERT: B 75 MET cc_start: 0.7510 (ptp) cc_final: 0.7209 (ptp) REVERT: B 89 MET cc_start: 0.8019 (mtp) cc_final: 0.7675 (mtp) REVERT: C 55 LEU cc_start: 0.9300 (tt) cc_final: 0.9087 (tt) REVERT: D 73 GLN cc_start: 0.8624 (tp40) cc_final: 0.8334 (tp-100) REVERT: D 84 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7950 (tp30) REVERT: D 250 ASP cc_start: 0.8303 (t0) cc_final: 0.8059 (t0) REVERT: E 126 MET cc_start: 0.9157 (tpp) cc_final: 0.8841 (tpp) REVERT: F 86 LYS cc_start: 0.8876 (pttt) cc_final: 0.8531 (tmtt) REVERT: F 93 ASP cc_start: 0.7719 (p0) cc_final: 0.6978 (t70) REVERT: G 145 ASP cc_start: 0.8583 (t0) cc_final: 0.7688 (p0) REVERT: H 27 LYS cc_start: 0.7335 (ttmt) cc_final: 0.7083 (ttpt) REVERT: H 85 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8271 (tp30) REVERT: H 90 TYR cc_start: 0.4105 (m-10) cc_final: 0.3463 (m-10) REVERT: I 91 ASN cc_start: 0.8462 (p0) cc_final: 0.7180 (m110) REVERT: J 53 LYS cc_start: 0.7249 (mptt) cc_final: 0.6913 (ptpt) REVERT: J 141 MET cc_start: 0.2257 (pmm) cc_final: 0.0225 (ptp) REVERT: K 88 GLN cc_start: 0.6823 (tp-100) cc_final: 0.6562 (pp30) REVERT: K 109 GLU cc_start: 0.7241 (mp0) cc_final: 0.6580 (mp0) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.2789 time to fit residues: 142.4815 Evaluate side-chains 269 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 2.9990 chunk 177 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 197 optimal weight: 30.0000 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 ASN E 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16132 Z= 0.196 Angle : 0.664 9.203 21948 Z= 0.332 Chirality : 0.045 0.220 2652 Planarity : 0.005 0.052 2762 Dihedral : 7.100 78.594 2296 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.82 % Favored : 89.98 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.19), residues: 2056 helix: 0.43 (0.19), residues: 850 sheet: -2.01 (0.31), residues: 267 loop : -2.76 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 168 HIS 0.004 0.001 HIS B 62 PHE 0.023 0.002 PHE E 16 TYR 0.029 0.001 TYR B 261 ARG 0.008 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 6 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 352 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7741 (pm20) cc_final: 0.7391 (pm20) REVERT: A 135 MET cc_start: 0.9244 (mmm) cc_final: 0.8983 (tpp) REVERT: A 194 ASP cc_start: 0.7611 (p0) cc_final: 0.6946 (p0) REVERT: B 75 MET cc_start: 0.7521 (ptp) cc_final: 0.7180 (ptp) REVERT: B 89 MET cc_start: 0.7984 (mtp) cc_final: 0.7653 (mtp) REVERT: C 31 MET cc_start: 0.8785 (mtt) cc_final: 0.8548 (mtp) REVERT: C 55 LEU cc_start: 0.9312 (tt) cc_final: 0.9103 (tt) REVERT: D 73 GLN cc_start: 0.8584 (tp40) cc_final: 0.8374 (tp-100) REVERT: D 84 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8071 (tp30) REVERT: E 16 PHE cc_start: 0.6610 (m-80) cc_final: 0.5882 (m-80) REVERT: E 126 MET cc_start: 0.9243 (tpp) cc_final: 0.8873 (tpp) REVERT: E 261 TYR cc_start: 0.7222 (m-80) cc_final: 0.6904 (m-10) REVERT: F 86 LYS cc_start: 0.8899 (pttt) cc_final: 0.8548 (tmtt) REVERT: F 93 ASP cc_start: 0.7800 (p0) cc_final: 0.7215 (t70) REVERT: G 72 THR cc_start: 0.6857 (p) cc_final: 0.5489 (p) REVERT: G 81 ARG cc_start: 0.7528 (ttp80) cc_final: 0.7076 (ttp80) REVERT: G 90 TYR cc_start: 0.6350 (m-80) cc_final: 0.6056 (m-80) REVERT: G 112 LEU cc_start: 0.5905 (tp) cc_final: 0.4992 (tt) REVERT: G 145 ASP cc_start: 0.8528 (t0) cc_final: 0.7685 (p0) REVERT: H 90 TYR cc_start: 0.4056 (m-10) cc_final: 0.3425 (m-10) REVERT: I 91 ASN cc_start: 0.8356 (p0) cc_final: 0.7049 (m-40) REVERT: J 53 LYS cc_start: 0.7250 (mptt) cc_final: 0.6891 (ptpt) REVERT: J 141 MET cc_start: 0.2398 (pmm) cc_final: 0.0619 (ptp) REVERT: L 84 LEU cc_start: 0.7545 (mm) cc_final: 0.7317 (mm) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.2619 time to fit residues: 135.9815 Evaluate side-chains 270 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 166 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 196 optimal weight: 0.0370 chunk 123 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 90 optimal weight: 0.0170 overall best weight: 3.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN C 60 HIS E 175 GLN H 149 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16132 Z= 0.240 Angle : 0.707 9.661 21948 Z= 0.353 Chirality : 0.047 0.298 2652 Planarity : 0.005 0.080 2762 Dihedral : 7.117 80.171 2296 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.26 % Favored : 89.49 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.19), residues: 2056 helix: 0.51 (0.19), residues: 846 sheet: -2.01 (0.31), residues: 276 loop : -2.76 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 29 HIS 0.004 0.001 HIS B 122 PHE 0.021 0.002 PHE B 16 TYR 0.019 0.001 TYR A 222 ARG 0.007 0.001 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 7 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 338 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.7820 (pm20) cc_final: 0.7486 (pm20) REVERT: A 194 ASP cc_start: 0.7483 (p0) cc_final: 0.6861 (p0) REVERT: A 198 ASP cc_start: 0.7637 (m-30) cc_final: 0.7421 (m-30) REVERT: B 89 MET cc_start: 0.7958 (mtp) cc_final: 0.7516 (mtp) REVERT: C 8 MET cc_start: 0.7913 (tpt) cc_final: 0.7661 (tpt) REVERT: C 39 ILE cc_start: 0.5218 (mm) cc_final: 0.4963 (mm) REVERT: D 84 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8046 (tp30) REVERT: E 126 MET cc_start: 0.9136 (tpp) cc_final: 0.8797 (tpp) REVERT: G 90 TYR cc_start: 0.6260 (m-80) cc_final: 0.5975 (m-80) REVERT: G 112 LEU cc_start: 0.6083 (tp) cc_final: 0.5167 (tt) REVERT: G 145 ASP cc_start: 0.8490 (t0) cc_final: 0.7699 (p0) REVERT: G 146 LEU cc_start: 0.6613 (pt) cc_final: 0.6402 (pt) REVERT: H 90 TYR cc_start: 0.4282 (m-10) cc_final: 0.3635 (m-10) REVERT: I 91 ASN cc_start: 0.8357 (p0) cc_final: 0.7029 (m-40) REVERT: J 53 LYS cc_start: 0.7219 (mptt) cc_final: 0.6887 (ptpt) REVERT: J 141 MET cc_start: 0.2485 (pmm) cc_final: 0.0719 (ptp) REVERT: L 84 LEU cc_start: 0.7665 (mm) cc_final: 0.7423 (mm) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.2724 time to fit residues: 135.2483 Evaluate side-chains 265 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.0503 > 50: distance: 60 - 62: 3.074 distance: 62 - 63: 22.788 distance: 63 - 64: 20.138 distance: 63 - 66: 18.039 distance: 64 - 65: 32.342 distance: 64 - 70: 6.718 distance: 66 - 67: 26.401 distance: 67 - 68: 19.546 distance: 67 - 69: 20.971 distance: 70 - 71: 9.432 distance: 71 - 72: 15.740 distance: 71 - 74: 9.143 distance: 72 - 73: 14.814 distance: 72 - 81: 9.321 distance: 74 - 75: 9.635 distance: 75 - 76: 12.018 distance: 76 - 77: 9.670 distance: 77 - 78: 4.221 distance: 78 - 79: 12.220 distance: 78 - 80: 8.898 distance: 81 - 82: 23.965 distance: 82 - 83: 9.128 distance: 83 - 84: 13.505 distance: 83 - 85: 14.943 distance: 85 - 86: 12.477 distance: 86 - 87: 12.530 distance: 86 - 89: 9.468 distance: 87 - 88: 12.321 distance: 87 - 90: 19.369 distance: 90 - 91: 12.631 distance: 91 - 92: 9.080 distance: 91 - 94: 6.838 distance: 92 - 93: 10.269 distance: 92 - 95: 10.031 distance: 95 - 96: 7.545 distance: 96 - 99: 8.755 distance: 97 - 98: 8.473 distance: 97 - 104: 9.494 distance: 99 - 100: 12.203 distance: 100 - 101: 7.592 distance: 101 - 102: 9.188 distance: 102 - 103: 6.525 distance: 104 - 105: 12.611 distance: 105 - 106: 31.103 distance: 105 - 108: 7.693 distance: 106 - 107: 21.730 distance: 106 - 112: 11.312 distance: 108 - 109: 26.648 distance: 109 - 110: 7.975 distance: 109 - 111: 22.302 distance: 113 - 114: 40.327 distance: 113 - 116: 9.777 distance: 114 - 115: 11.980 distance: 114 - 120: 8.394 distance: 116 - 117: 22.099 distance: 117 - 118: 25.428 distance: 118 - 119: 9.816 distance: 120 - 121: 10.119 distance: 120 - 126: 8.548 distance: 121 - 122: 17.091 distance: 121 - 124: 6.454 distance: 122 - 123: 14.774 distance: 122 - 127: 31.055 distance: 124 - 125: 7.871 distance: 125 - 126: 8.886 distance: 127 - 128: 11.859 distance: 128 - 129: 21.749 distance: 128 - 131: 12.123 distance: 129 - 130: 16.183 distance: 129 - 133: 4.679 distance: 131 - 132: 11.335