Starting phenix.real_space_refine on Wed Sep 25 11:45:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxa_20931/09_2024/6uxa_20931.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxa_20931/09_2024/6uxa_20931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxa_20931/09_2024/6uxa_20931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxa_20931/09_2024/6uxa_20931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxa_20931/09_2024/6uxa_20931.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uxa_20931/09_2024/6uxa_20931.cif" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 6136 2.51 5 N 2104 2.21 5 O 2104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10344 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 1494 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 18, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 28, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 484 Chain: "E" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 361 Chain: "C" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 1494 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 18, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 28, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 484 Chain: "G" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 361 Chain: "B" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 1494 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 18, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 28, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 484 Chain: "F" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 361 Chain: "D" Number of atoms: 1494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 1494 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 258} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain breaks: 1 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 908 Unresolved non-hydrogen angles: 1175 Unresolved non-hydrogen dihedrals: 731 Unresolved non-hydrogen chiralities: 107 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 18, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 3, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 28, 'ARG:plan': 22} Unresolved non-hydrogen planarities: 484 Chain: "H" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1092 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 190} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 654 Unresolved non-hydrogen angles: 833 Unresolved non-hydrogen dihedrals: 519 Unresolved non-hydrogen chiralities: 68 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 17, 'PHE:plan': 5, 'GLU:plan': 24, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 361 Time building chain proxies: 7.16, per 1000 atoms: 0.69 Number of scatterers: 10344 At special positions: 0 Unit cell: (138.03, 138.03, 120.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2104 8.00 N 2104 7.00 C 6136 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: 2.72 Conformation dependent library (CDL) restraints added in 2.0 seconds 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 16 sheets defined 51.5% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 19 through 43 Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 69 through 99 removed outlier: 4.893A pdb=" N GLY A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 148 through 156 Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.806A pdb=" N ALA A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.535A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 230 through 241 Processing helix chain 'A' and resid 246 through 256 removed outlier: 3.502A pdb=" N MET A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.832A pdb=" N VAL A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'E' and resid 124 through 133 Processing helix chain 'E' and resid 148 through 155 removed outlier: 3.813A pdb=" N SER E 155 " --> pdb=" O LYS E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 173 removed outlier: 3.705A pdb=" N ALA E 173 " --> pdb=" O ASP E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.649A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 224 removed outlier: 3.586A pdb=" N GLY E 224 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.592A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 256 removed outlier: 3.549A pdb=" N MET E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU E 256 " --> pdb=" O VAL E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 removed outlier: 3.563A pdb=" N ASP E 284 " --> pdb=" O VAL E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 323 through 334 Processing helix chain 'C' and resid 19 through 43 Processing helix chain 'C' and resid 45 through 58 Processing helix chain 'C' and resid 69 through 99 removed outlier: 4.892A pdb=" N GLY C 85 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 148 through 156 Processing helix chain 'C' and resid 166 through 173 removed outlier: 3.807A pdb=" N ALA C 173 " --> pdb=" O ASP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.535A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 230 through 241 Processing helix chain 'C' and resid 246 through 256 removed outlier: 3.502A pdb=" N MET C 250 " --> pdb=" O GLY C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 290 removed outlier: 3.831A pdb=" N VAL C 288 " --> pdb=" O ASP C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 334 Processing helix chain 'G' and resid 124 through 133 Processing helix chain 'G' and resid 148 through 155 removed outlier: 3.813A pdb=" N SER G 155 " --> pdb=" O LYS G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 173 removed outlier: 3.705A pdb=" N ALA G 173 " --> pdb=" O ASP G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.647A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 224 removed outlier: 3.588A pdb=" N GLY G 224 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.590A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 256 removed outlier: 3.548A pdb=" N MET G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU G 256 " --> pdb=" O VAL G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 removed outlier: 3.563A pdb=" N ASP G 284 " --> pdb=" O VAL G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 323 through 334 Processing helix chain 'B' and resid 19 through 43 Processing helix chain 'B' and resid 45 through 58 Processing helix chain 'B' and resid 69 through 99 removed outlier: 4.894A pdb=" N GLY B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE B 97 " --> pdb=" O ARG B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 148 through 156 Processing helix chain 'B' and resid 166 through 173 removed outlier: 3.791A pdb=" N ALA B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.693A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 242 removed outlier: 3.530A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 256 Processing helix chain 'B' and resid 279 through 284 Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'F' and resid 124 through 133 Processing helix chain 'F' and resid 148 through 154 Processing helix chain 'F' and resid 166 through 173 removed outlier: 3.941A pdb=" N ALA F 173 " --> pdb=" O ASP F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 removed outlier: 3.710A pdb=" N ILE F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.583A pdb=" N GLY F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 241 removed outlier: 3.564A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 256 removed outlier: 3.790A pdb=" N LEU F 256 " --> pdb=" O VAL F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 284 removed outlier: 3.599A pdb=" N ASP F 284 " --> pdb=" O VAL F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.584A pdb=" N VAL F 288 " --> pdb=" O ASP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 334 Processing helix chain 'D' and resid 19 through 43 Processing helix chain 'D' and resid 45 through 58 Processing helix chain 'D' and resid 69 through 99 removed outlier: 4.894A pdb=" N GLY D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 96 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 97 " --> pdb=" O ARG D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 134 Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 148 through 156 Processing helix chain 'D' and resid 166 through 173 removed outlier: 3.790A pdb=" N ALA D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.694A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 242 removed outlier: 3.531A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 256 Processing helix chain 'D' and resid 279 through 284 Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 323 through 334 Processing helix chain 'H' and resid 124 through 133 Processing helix chain 'H' and resid 148 through 154 Processing helix chain 'H' and resid 166 through 173 removed outlier: 3.941A pdb=" N ALA H 173 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 removed outlier: 3.708A pdb=" N ILE H 201 " --> pdb=" O GLY H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.583A pdb=" N GLY H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 241 removed outlier: 3.564A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 256 removed outlier: 3.788A pdb=" N LEU H 256 " --> pdb=" O VAL H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 279 through 284 removed outlier: 3.599A pdb=" N ASP H 284 " --> pdb=" O VAL H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.582A pdb=" N VAL H 288 " --> pdb=" O ASP H 284 " (cutoff:3.500A) Processing helix chain 'H' and resid 323 through 334 Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.408A pdb=" N VAL A 139 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL A 160 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL A 141 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 7.390A pdb=" N ILE A 321 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE A 293 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 158 through 161 removed outlier: 6.499A pdb=" N VAL E 139 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL E 160 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL E 141 " --> pdb=" O VAL E 160 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL E 181 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N GLU E 210 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL E 183 " --> pdb=" O GLU E 210 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE E 207 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE E 229 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA E 209 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 263 through 268 removed outlier: 7.219A pdb=" N ILE E 321 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ILE E 293 " --> pdb=" O ILE E 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.407A pdb=" N VAL C 139 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL C 160 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL C 141 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.720A pdb=" N ILE C 317 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL C 296 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.498A pdb=" N VAL G 139 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N VAL G 160 " --> pdb=" O VAL G 139 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL G 141 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL G 181 " --> pdb=" O ILE G 208 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N GLU G 210 " --> pdb=" O VAL G 181 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL G 183 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE G 207 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ILE G 229 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA G 209 " --> pdb=" O ILE G 229 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 263 through 268 removed outlier: 7.220A pdb=" N ILE G 321 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N ILE G 293 " --> pdb=" O ILE G 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.549A pdb=" N VAL B 139 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N HIS B 117 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 180 " --> pdb=" O HIS B 117 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE B 208 " --> pdb=" O ARG B 179 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL B 181 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N GLU B 210 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL B 183 " --> pdb=" O GLU B 210 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE B 207 " --> pdb=" O GLN B 227 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE B 229 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA B 209 " --> pdb=" O ILE B 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 263 through 268 removed outlier: 7.239A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 158 through 161 removed outlier: 6.392A pdb=" N VAL F 139 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 263 through 268 removed outlier: 7.229A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 158 through 161 removed outlier: 6.548A pdb=" N VAL D 139 " --> pdb=" O ASN D 158 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N HIS D 117 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA D 180 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE D 208 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL D 181 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N GLU D 210 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL D 183 " --> pdb=" O GLU D 210 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE D 207 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE D 229 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA D 209 " --> pdb=" O ILE D 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 268 removed outlier: 7.238A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 158 through 161 removed outlier: 6.391A pdb=" N VAL H 139 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 7.231A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 813 hydrogen bonds defined for protein. 2355 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: 3.56 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 2104 1.28 - 1.36: 2092 1.36 - 1.43: 0 1.43 - 1.51: 2112 1.51 - 1.58: 4024 Bond restraints: 10332 Sorted by residual: bond pdb=" C VAL A 60 " pdb=" O VAL A 60 " ideal model delta sigma weight residual 1.237 1.268 -0.031 1.12e-02 7.97e+03 7.88e+00 bond pdb=" C VAL D 60 " pdb=" O VAL D 60 " ideal model delta sigma weight residual 1.237 1.268 -0.031 1.12e-02 7.97e+03 7.79e+00 bond pdb=" CA VAL A 55 " pdb=" CB VAL A 55 " ideal model delta sigma weight residual 1.542 1.579 -0.038 1.45e-02 4.76e+03 6.80e+00 bond pdb=" C VAL C 60 " pdb=" O VAL C 60 " ideal model delta sigma weight residual 1.237 1.265 -0.029 1.12e-02 7.97e+03 6.53e+00 bond pdb=" CA VAL B 55 " pdb=" CB VAL B 55 " ideal model delta sigma weight residual 1.542 1.578 -0.037 1.45e-02 4.76e+03 6.39e+00 ... (remaining 10327 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 11879 0.93 - 1.86: 2003 1.86 - 2.79: 332 2.79 - 3.72: 97 3.72 - 4.65: 29 Bond angle restraints: 14340 Sorted by residual: angle pdb=" C SER D 66 " pdb=" N PRO D 67 " pdb=" CA PRO D 67 " ideal model delta sigma weight residual 119.76 116.53 3.23 1.00e+00 1.00e+00 1.04e+01 angle pdb=" C SER B 66 " pdb=" N PRO B 67 " pdb=" CA PRO B 67 " ideal model delta sigma weight residual 119.76 116.57 3.19 1.00e+00 1.00e+00 1.02e+01 angle pdb=" C SER C 66 " pdb=" N PRO C 67 " pdb=" CA PRO C 67 " ideal model delta sigma weight residual 119.76 116.63 3.13 1.00e+00 1.00e+00 9.77e+00 angle pdb=" N GLU D 171 " pdb=" CA GLU D 171 " pdb=" C GLU D 171 " ideal model delta sigma weight residual 111.28 114.63 -3.35 1.09e+00 8.42e-01 9.45e+00 angle pdb=" N GLU B 171 " pdb=" CA GLU B 171 " pdb=" C GLU B 171 " ideal model delta sigma weight residual 111.28 114.63 -3.35 1.09e+00 8.42e-01 9.44e+00 ... (remaining 14335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 3.04: 4804 3.04 - 6.08: 765 6.08 - 9.11: 256 9.11 - 12.15: 95 12.15 - 15.19: 28 Dihedral angle restraints: 5948 sinusoidal: 0 harmonic: 5948 Sorted by residual: dihedral pdb=" C VAL A 27 " pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" CB VAL A 27 " ideal model delta harmonic sigma weight residual -122.00 -131.25 9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C VAL B 27 " pdb=" N VAL B 27 " pdb=" CA VAL B 27 " pdb=" CB VAL B 27 " ideal model delta harmonic sigma weight residual -122.00 -131.22 9.22 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" C VAL C 27 " pdb=" N VAL C 27 " pdb=" CA VAL C 27 " pdb=" CB VAL C 27 " ideal model delta harmonic sigma weight residual -122.00 -131.20 9.20 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 5945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1372 0.060 - 0.119: 430 0.119 - 0.179: 112 0.179 - 0.239: 10 0.239 - 0.298: 4 Chirality restraints: 1928 Sorted by residual: chirality pdb=" CA THR B 59 " pdb=" N THR B 59 " pdb=" C THR B 59 " pdb=" CB THR B 59 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CA THR A 59 " pdb=" N THR A 59 " pdb=" C THR A 59 " pdb=" CB THR A 59 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA THR C 59 " pdb=" N THR C 59 " pdb=" C THR C 59 " pdb=" CB THR C 59 " both_signs ideal model delta sigma weight residual False 2.53 2.23 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 1925 not shown) Planarity restraints: 2092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 169 " 0.014 2.00e-02 2.50e+03 2.93e-02 8.58e+00 pdb=" C ASP B 169 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP B 169 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU B 170 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 169 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C ASP D 169 " -0.050 2.00e-02 2.50e+03 pdb=" O ASP D 169 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU D 170 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 267 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C VAL B 267 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL B 267 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO B 268 " 0.011 2.00e-02 2.50e+03 ... (remaining 2089 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 6551 3.09 - 3.54: 10954 3.54 - 4.00: 12158 4.00 - 4.45: 13949 4.45 - 4.90: 22647 Nonbonded interactions: 66259 Sorted by model distance: nonbonded pdb=" N GLY G 136 " pdb=" N SER G 137 " model vdw 2.638 2.560 nonbonded pdb=" N GLY E 136 " pdb=" N SER E 137 " model vdw 2.638 2.560 nonbonded pdb=" N SER B 66 " pdb=" O SER B 66 " model vdw 2.640 2.496 nonbonded pdb=" N SER D 66 " pdb=" O SER D 66 " model vdw 2.640 2.496 nonbonded pdb=" N VAL D 181 " pdb=" O ARG D 206 " model vdw 2.640 3.120 ... (remaining 66254 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 2 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } pdb_interpretation.ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. 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: 1.730 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.110 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 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 : 0.005 0.041 10332 Z= 0.341 Angle : 0.775 4.654 14340 Z= 0.537 Chirality : 0.063 0.298 1928 Planarity : 0.004 0.029 2092 Dihedral : 4.562 15.189 2092 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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: -2.56 (0.15), residues: 2080 helix: -1.92 (0.13), residues: 1080 sheet: 0.64 (0.25), residues: 336 loop : -2.29 (0.17), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4160 Ramachandran restraints generated. 2080 Oldfield, 0 Emsley, 2080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.171 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0327 time to fit residues: 0.4920 Evaluate side-chains 5 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.157 Evaluate side-chains 4 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.131 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0158 time to fit residues: 0.3142 Evaluate side-chains 4 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 53 optimal weight: 30.0000 chunk 106 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 163 optimal weight: 50.0000 chunk 63 optimal weight: 30.0000 chunk 99 optimal weight: 20.0000 chunk 121 optimal weight: 20.0000 chunk 188 optimal weight: 20.0000 overall best weight: 7.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5749 moved from start: 1.6279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10332 Z= 0.353 Angle : 0.727 9.069 14340 Z= 0.486 Chirality : 0.047 0.134 1928 Planarity : 0.005 0.042 2092 Dihedral : 5.552 26.121 2092 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.50 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.17), residues: 2080 helix: -0.12 (0.15), residues: 1080 sheet: 1.03 (0.25), residues: 332 loop : -1.19 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4128 Ramachandran restraints generated. 2064 Oldfield, 0 Emsley, 2064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.167 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0178 time to fit residues: 0.4031 Evaluate side-chains 5 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.167 Evaluate side-chains 4 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.125 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0144 time to fit residues: 0.2852 Evaluate side-chains 4 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 50.0000 chunk 58 optimal weight: 8.9990 chunk 157 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 52 optimal weight: 50.0000 chunk 189 optimal weight: 20.0000 chunk 204 optimal weight: 30.0000 chunk 168 optimal weight: 10.0000 chunk 187 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6048 moved from start: 1.6857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.017 10332 Z= 0.367 Angle : 0.737 7.163 14340 Z= 0.497 Chirality : 0.048 0.137 1928 Planarity : 0.006 0.030 2092 Dihedral : 5.881 22.095 2092 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.38 % Favored : 94.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.18), residues: 2080 helix: -0.00 (0.16), residues: 1048 sheet: 0.37 (0.31), residues: 276 loop : -1.31 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.000 0.000 TRP A 46 PHE 0.000 0.000 PHE A 38 TYR 0.000 0.000 TYR A 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3688 Ramachandran restraints generated. 1844 Oldfield, 0 Emsley, 1844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.165 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0171 time to fit residues: 0.3841 Evaluate side-chains 5 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.165 Evaluate side-chains 4 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.113 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0134 time to fit residues: 0.2610 Evaluate side-chains 4 residues out of total 190 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 800, in minimization_ncs ncs_groups = ncs_groups) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 400, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 133, in refine refine_sites = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 434, in __init__ ignore_line_search_failed_maxfev=True)) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 459, in compute_functional_and_gradients x=self.x) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 248, in target_and_gradients grad = g_data) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/mmtbx/refinement/minimization_ncs_constraints.py", line 112, in restraints_target_and_grads compute_gradients = True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.8203 > 50: distance: 1 - 2: 3.434 distance: 2 - 3: 5.741 distance: 2 - 5: 4.530 distance: 3 - 20: 11.824 distance: 6 - 7: 6.665 distance: 6 - 9: 16.875 distance: 7 - 8: 15.777 distance: 7 - 10: 6.579 distance: 8 - 24: 11.877 distance: 10 - 11: 8.573 distance: 11 - 12: 16.908 distance: 11 - 14: 24.713 distance: 12 - 13: 11.500 distance: 12 - 15: 10.321 distance: 13 - 29: 20.301 distance: 15 - 16: 13.259 distance: 16 - 17: 5.090 distance: 16 - 19: 6.951 distance: 17 - 18: 13.090 distance: 17 - 20: 9.972 distance: 18 - 34: 33.514 distance: 20 - 21: 16.897 distance: 21 - 22: 18.340 distance: 22 - 23: 23.653 distance: 22 - 24: 17.182 distance: 23 - 39: 22.935 distance: 24 - 25: 12.071 distance: 25 - 26: 6.923 distance: 25 - 28: 31.964 distance: 26 - 27: 25.633 distance: 26 - 29: 17.255 distance: 27 - 44: 17.626 distance: 29 - 30: 37.948 distance: 30 - 31: 7.449 distance: 30 - 33: 29.460 distance: 31 - 32: 20.913 distance: 31 - 34: 22.643 distance: 34 - 35: 22.956 distance: 35 - 36: 16.360 distance: 35 - 38: 9.763 distance: 36 - 37: 13.493 distance: 36 - 39: 14.902 distance: 39 - 40: 23.026 distance: 40 - 41: 11.855 distance: 40 - 43: 4.548 distance: 41 - 42: 13.221 distance: 41 - 44: 12.015 distance: 44 - 45: 6.369 distance: 45 - 46: 10.311 distance: 45 - 48: 10.966