Starting phenix.real_space_refine on Sun Aug 4 07:41:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr9_22444/08_2024/7jr9_22444.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr9_22444/08_2024/7jr9_22444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr9_22444/08_2024/7jr9_22444.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr9_22444/08_2024/7jr9_22444.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr9_22444/08_2024/7jr9_22444.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jr9_22444/08_2024/7jr9_22444.cif" } resolution = 2.95 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 6391 2.51 5 N 1706 2.21 5 O 1887 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 230": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D ARG 398": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 205": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10021 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1970 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 12, 'TRANS': 241} Chain breaks: 1 Chain: "B" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1946 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 11, 'TRANS': 239} Chain breaks: 1 Chain: "C" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2110 Classifications: {'peptide': 280} Link IDs: {'PTRANS': 22, 'TRANS': 257} Chain breaks: 3 Chain: "D" Number of atoms: 2574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2574 Classifications: {'peptide': 339} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 301} Chain breaks: 2 Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 1351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1351 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 6.81, per 1000 atoms: 0.68 Number of scatterers: 10021 At special positions: 0 Unit cell: (88.92, 97.47, 164.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1887 8.00 N 1706 7.00 C 6391 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 155 " distance=2.02 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: 3.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2370 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 18 sheets defined 23.4% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 7 through 16 Processing helix chain 'A' and resid 17 through 19 No H-bonds generated for 'chain 'A' and resid 17 through 19' Processing helix chain 'A' and resid 23 through 41 removed outlier: 3.755A pdb=" N HIS A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 210 through 214 removed outlier: 3.531A pdb=" N GLN A 213 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 23 through 42 removed outlier: 3.567A pdb=" N ALA B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Proline residue: B 35 - end of helix Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.995A pdb=" N THR B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 145 Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.913A pdb=" N ASN C 214 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 245 removed outlier: 3.647A pdb=" N ARG C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 283 removed outlier: 3.542A pdb=" N VAL C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 315 removed outlier: 4.006A pdb=" N ALA C 315 " --> pdb=" O GLU C 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 125 through 142 Processing helix chain 'D' and resid 191 through 195 Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 246 through 263 removed outlier: 3.711A pdb=" N VAL D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.631A pdb=" N GLU D 292 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.686A pdb=" N ASP D 349 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 85 removed outlier: 3.536A pdb=" N GLU A 79 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL A 68 " --> pdb=" O GLU A 79 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS A 81 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N TYR A 66 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE A 83 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N GLU A 64 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N SER A 85 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N VAL A 62 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU A 64 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU A 48 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N TYR A 66 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N LEU A 46 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 16.418A pdb=" N TRP A 251 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N THR A 47 " --> pdb=" O TRP A 251 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N SER A 253 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TRP A 49 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N TYR A 240 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 123 Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 174 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 93 removed outlier: 5.798A pdb=" N ALA B 75 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER B 71 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 77 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA B 69 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU B 79 " --> pdb=" O ASN B 67 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN B 67 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N GLU B 64 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LEU B 48 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N TYR B 66 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LEU B 46 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 16.010A pdb=" N TRP B 251 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 11.177A pdb=" N THR B 47 " --> pdb=" O TRP B 251 " (cutoff:3.500A) removed outlier: 9.774A pdb=" N SER B 253 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TRP B 49 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR B 240 " --> pdb=" O SER B 234 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL B 229 " --> pdb=" O ASP B 224 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 119 through 123 Processing sheet with id=AA7, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AA8, first strand: chain 'B' and resid 172 through 174 Processing sheet with id=AA9, first strand: chain 'C' and resid 229 through 230 removed outlier: 6.458A pdb=" N TYR C 167 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS C 159 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL C 169 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.448A pdb=" N ARG C 155 " --> pdb=" O CYS C 414 " (cutoff:3.500A) removed outlier: 9.895A pdb=" N TYR C 416 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE C 157 " --> pdb=" O TYR C 416 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N GLY C 418 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LYS C 159 " --> pdb=" O GLY C 418 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ALA C 403 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AB2, first strand: chain 'C' and resid 290 through 292 Processing sheet with id=AB3, first strand: chain 'D' and resid 209 through 210 removed outlier: 6.515A pdb=" N TYR D 163 " --> pdb=" O LYS D 155 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS D 155 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL D 165 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR D 149 " --> pdb=" O THR D 169 " (cutoff:3.500A) removed outlier: 21.775A pdb=" N PHE D 400 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 16.070A pdb=" N THR D 149 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 14.927A pdb=" N SER D 402 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 9.346A pdb=" N ARG D 151 " --> pdb=" O SER D 402 " (cutoff:3.500A) removed outlier: 9.723A pdb=" N TYR D 404 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE D 153 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N GLY D 406 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LYS D 155 " --> pdb=" O GLY D 406 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 264 through 266 Processing sheet with id=AB5, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AB6, first strand: chain 'D' and resid 365 through 369 Processing sheet with id=AB7, first strand: chain 'G' and resid -3 through -1 removed outlier: 3.560A pdb=" N UNK G -3 " --> pdb=" O GLU E 29 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU E 29 " --> pdb=" O UNK G -3 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 50 through 53 removed outlier: 5.893A pdb=" N THR E 51 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR E 58 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 56 " --> pdb=" O GLU E 53 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS E 84 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL E 77 " --> pdb=" O HIS E 82 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS E 82 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY E 97 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN E 107 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS E 130 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP E 123 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N HIS E 128 " --> pdb=" O TRP E 123 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN E 141 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP E 156 " --> pdb=" O GLN E 141 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL E 143 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY E 154 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP E 145 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR E 152 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR E 178 " --> pdb=" O PHE E 195 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 50 through 53 removed outlier: 5.893A pdb=" N THR E 51 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR E 58 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 56 " --> pdb=" O GLU E 53 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LYS E 84 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL E 77 " --> pdb=" O HIS E 82 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N HIS E 82 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY E 97 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN E 107 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LYS E 130 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N TRP E 123 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N HIS E 128 " --> pdb=" O TRP E 123 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLN E 141 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP E 156 " --> pdb=" O GLN E 141 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL E 143 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLY E 154 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP E 145 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N THR E 152 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N THR E 178 " --> pdb=" O PHE E 195 " (cutoff:3.500A) 428 hydrogen bonds defined for protein. 1173 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: 3.15 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3191 1.34 - 1.45: 1777 1.45 - 1.57: 5256 1.57 - 1.69: 0 1.69 - 1.80: 56 Bond restraints: 10280 Sorted by residual: bond pdb=" C ALA D 294 " pdb=" N LEU D 295 " ideal model delta sigma weight residual 1.332 1.289 0.042 1.92e-02 2.71e+03 4.89e+00 bond pdb=" CA GLY D 121 " pdb=" C GLY D 121 " ideal model delta sigma weight residual 1.514 1.489 0.025 1.41e-02 5.03e+03 3.25e+00 bond pdb=" CG LEU D 134 " pdb=" CD1 LEU D 134 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CB ARG C 396 " pdb=" CG ARG C 396 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.52e+00 bond pdb=" C THR E 111 " pdb=" N TYR E 112 " ideal model delta sigma weight residual 1.329 1.300 0.029 1.86e-02 2.89e+03 2.36e+00 ... (remaining 10275 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.37: 401 106.37 - 113.29: 5379 113.29 - 120.21: 3724 120.21 - 127.13: 4333 127.13 - 134.05: 148 Bond angle restraints: 13985 Sorted by residual: angle pdb=" C THR E 111 " pdb=" N TYR E 112 " pdb=" CA TYR E 112 " ideal model delta sigma weight residual 121.48 128.38 -6.90 2.04e+00 2.40e-01 1.14e+01 angle pdb=" C VAL B 157 " pdb=" N ASP B 158 " pdb=" CA ASP B 158 " ideal model delta sigma weight residual 121.58 115.41 6.17 1.95e+00 2.63e-01 1.00e+01 angle pdb=" CA TYR A 78 " pdb=" CB TYR A 78 " pdb=" CG TYR A 78 " ideal model delta sigma weight residual 113.90 119.52 -5.62 1.80e+00 3.09e-01 9.74e+00 angle pdb=" C GLY C 372 " pdb=" N GLU C 373 " pdb=" CA GLU C 373 " ideal model delta sigma weight residual 122.40 126.92 -4.52 1.45e+00 4.76e-01 9.73e+00 angle pdb=" C THR B 164 " pdb=" N SER B 165 " pdb=" CA SER B 165 " ideal model delta sigma weight residual 122.82 127.22 -4.40 1.42e+00 4.96e-01 9.60e+00 ... (remaining 13980 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 5821 14.84 - 29.68: 186 29.68 - 44.52: 24 44.52 - 59.35: 1 59.35 - 74.19: 5 Dihedral angle restraints: 6037 sinusoidal: 2309 harmonic: 3728 Sorted by residual: dihedral pdb=" CA TYR C 260 " pdb=" C TYR C 260 " pdb=" N PRO C 261 " pdb=" CA PRO C 261 " ideal model delta harmonic sigma weight residual 180.00 154.62 25.38 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA THR D 168 " pdb=" C THR D 168 " pdb=" N THR D 169 " pdb=" CA THR D 169 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA SER A 92 " pdb=" C SER A 92 " pdb=" N ASP A 93 " pdb=" CA ASP A 93 " ideal model delta harmonic sigma weight residual 180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 6034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1073 0.052 - 0.105: 355 0.105 - 0.157: 63 0.157 - 0.210: 9 0.210 - 0.262: 3 Chirality restraints: 1503 Sorted by residual: chirality pdb=" CB VAL E 71 " pdb=" CA VAL E 71 " pdb=" CG1 VAL E 71 " pdb=" CG2 VAL E 71 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB VAL E 88 " pdb=" CA VAL E 88 " pdb=" CG1 VAL E 88 " pdb=" CG2 VAL E 88 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" CB ILE B 8 " pdb=" CA ILE B 8 " pdb=" CG1 ILE B 8 " pdb=" CG2 ILE B 8 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1500 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 184 " -0.022 2.00e-02 2.50e+03 1.97e-02 7.76e+00 pdb=" CG TYR E 184 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR E 184 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR E 184 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 184 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR E 184 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 184 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR E 184 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 168 " -0.010 2.00e-02 2.50e+03 1.93e-02 6.52e+00 pdb=" CG PHE E 168 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE E 168 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE E 168 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE E 168 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE E 168 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE E 168 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 78 " -0.018 2.00e-02 2.50e+03 1.79e-02 6.42e+00 pdb=" CG TYR B 78 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR B 78 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR B 78 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 78 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 78 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 78 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 78 " 0.001 2.00e-02 2.50e+03 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1999 2.77 - 3.30: 8334 3.30 - 3.83: 16447 3.83 - 4.37: 19983 4.37 - 4.90: 34353 Nonbonded interactions: 81116 Sorted by model distance: nonbonded pdb=" OG SER C 383 " pdb=" OE1 GLN C 391 " model vdw 2.235 3.040 nonbonded pdb=" OG SER A 234 " pdb=" O PHE A 237 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR A 255 " pdb=" O ASP A 258 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR D 230 " pdb=" OE1 GLU D 247 " model vdw 2.300 3.040 nonbonded pdb=" OG1 THR C 250 " pdb=" OE1 GLU C 267 " model vdw 2.313 3.040 ... (remaining 81111 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 124 or resid 142 through 269)) selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.310 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 10280 Z= 0.513 Angle : 0.815 7.675 13985 Z= 0.459 Chirality : 0.054 0.262 1503 Planarity : 0.008 0.055 1828 Dihedral : 8.260 74.192 3664 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -2.53 (0.20), residues: 1274 helix: -2.33 (0.23), residues: 266 sheet: -1.43 (0.26), residues: 310 loop : -1.46 (0.20), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 156 HIS 0.006 0.002 HIS C 321 PHE 0.040 0.004 PHE E 168 TYR 0.048 0.004 TYR E 184 ARG 0.015 0.002 ARG D 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 325 HIS cc_start: 0.7901 (p-80) cc_final: 0.7218 (t-170) REVERT: E 87 MET cc_start: 0.7786 (tpt) cc_final: 0.6798 (tpt) REVERT: E 119 GLN cc_start: 0.7860 (mt0) cc_final: 0.7575 (mt0) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.5703 time to fit residues: 292.2337 Evaluate side-chains 73 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN C 80 GLN C 238 GLN C 374 GLN C 391 GLN ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10280 Z= 0.186 Angle : 0.530 7.906 13985 Z= 0.278 Chirality : 0.040 0.148 1503 Planarity : 0.005 0.041 1828 Dihedral : 4.430 17.443 1422 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.66 % Allowed : 8.71 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -1.25 (0.22), residues: 1274 helix: -0.59 (0.29), residues: 276 sheet: -0.95 (0.28), residues: 294 loop : -0.78 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 415 HIS 0.002 0.001 HIS B 200 PHE 0.010 0.001 PHE A 267 TYR 0.017 0.002 TYR B 255 ARG 0.003 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 303 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: C 325 HIS cc_start: 0.7915 (p-80) cc_final: 0.7275 (t-170) REVERT: C 366 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: E 87 MET cc_start: 0.7735 (tpt) cc_final: 0.7018 (tpt) outliers start: 17 outliers final: 4 residues processed: 91 average time/residue: 1.5182 time to fit residues: 147.0567 Evaluate side-chains 73 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 303 GLU Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 200 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 103 optimal weight: 0.0980 chunk 115 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 93 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10280 Z= 0.154 Angle : 0.487 7.043 13985 Z= 0.251 Chirality : 0.039 0.139 1503 Planarity : 0.004 0.033 1828 Dihedral : 4.064 16.821 1422 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.86 % Allowed : 9.59 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: -0.61 (0.22), residues: 1274 helix: 0.23 (0.31), residues: 276 sheet: -0.59 (0.28), residues: 287 loop : -0.49 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 99 HIS 0.002 0.001 HIS E 134 PHE 0.010 0.001 PHE A 267 TYR 0.013 0.001 TYR D 198 ARG 0.002 0.000 ARG C 244 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 ILE cc_start: 0.9176 (tp) cc_final: 0.8898 (pt) REVERT: C 211 LYS cc_start: 0.8400 (ptmt) cc_final: 0.8176 (ptmt) REVERT: C 325 HIS cc_start: 0.7937 (p-80) cc_final: 0.7268 (t-170) REVERT: C 366 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: E 57 ARG cc_start: 0.7546 (mtm180) cc_final: 0.7176 (mtm-85) outliers start: 19 outliers final: 7 residues processed: 88 average time/residue: 1.5456 time to fit residues: 145.0002 Evaluate side-chains 76 residues out of total 1023 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 68 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LYS Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain C residue 366 GLU Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 200 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/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-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-5409/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-5409/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-5409/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-5409/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: 61.1314 > 50: distance: 10 - 14: 23.950 distance: 14 - 15: 36.686 distance: 15 - 16: 29.087 distance: 15 - 18: 26.535 distance: 16 - 17: 42.483 distance: 16 - 22: 16.566 distance: 18 - 19: 44.624 distance: 19 - 20: 54.420 distance: 19 - 21: 60.902 distance: 22 - 23: 17.348 distance: 22 - 28: 23.576 distance: 23 - 24: 7.091 distance: 23 - 26: 19.455 distance: 24 - 25: 7.238 distance: 24 - 29: 20.971 distance: 26 - 27: 36.019 distance: 27 - 28: 16.862 distance: 29 - 30: 22.011 distance: 30 - 31: 29.241 distance: 30 - 33: 23.484 distance: 31 - 32: 13.361 distance: 31 - 37: 43.139 distance: 33 - 34: 25.601 distance: 34 - 35: 16.734 distance: 34 - 36: 10.998 distance: 37 - 38: 13.305 distance: 38 - 39: 41.182 distance: 38 - 41: 19.995 distance: 39 - 40: 33.501 distance: 39 - 45: 27.345 distance: 41 - 42: 58.406 distance: 42 - 43: 20.404 distance: 43 - 44: 34.317 distance: 45 - 46: 22.639 distance: 45 - 51: 32.025 distance: 46 - 47: 4.669 distance: 46 - 49: 20.469 distance: 47 - 48: 19.265 distance: 47 - 52: 25.763 distance: 49 - 50: 22.962 distance: 50 - 51: 11.867 distance: 52 - 53: 29.277 distance: 53 - 54: 14.474 distance: 53 - 56: 12.885 distance: 54 - 55: 23.914 distance: 54 - 61: 31.587 distance: 56 - 57: 23.510 distance: 57 - 58: 7.708 distance: 58 - 59: 13.647 distance: 58 - 60: 22.714 distance: 61 - 62: 15.129 distance: 62 - 63: 21.365 distance: 62 - 65: 26.292 distance: 63 - 64: 16.854 distance: 63 - 66: 15.840 distance: 66 - 67: 25.831 distance: 66 - 72: 14.594 distance: 67 - 68: 27.354 distance: 67 - 70: 22.688 distance: 68 - 69: 33.325 distance: 68 - 73: 21.197 distance: 70 - 71: 51.157 distance: 71 - 72: 28.970 distance: 73 - 74: 11.879 distance: 74 - 75: 15.195 distance: 74 - 77: 18.450 distance: 75 - 76: 29.960 distance: 75 - 82: 15.888 distance: 77 - 78: 31.866 distance: 78 - 79: 32.122 distance: 79 - 80: 5.470 distance: 79 - 81: 31.764 distance: 82 - 83: 32.543 distance: 83 - 84: 13.334 distance: 84 - 85: 3.892 distance: 84 - 86: 18.295