Starting phenix.real_space_refine on Mon Mar 18 12:03:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oll_20116/03_2024/6oll_20116.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oll_20116/03_2024/6oll_20116.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oll_20116/03_2024/6oll_20116.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oll_20116/03_2024/6oll_20116.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oll_20116/03_2024/6oll_20116.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oll_20116/03_2024/6oll_20116.pdb" } resolution = 4.1 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= 0.005 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10416 atoms to isotropic. 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 6198 2.51 5 N 2114 2.21 5 O 2114 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10426 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1741 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1362 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "B" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 1731 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 20, 'TRANS': 330} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1063 Unresolved non-hydrogen angles: 1358 Unresolved non-hydrogen dihedrals: 853 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "C" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1741 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PTRANS': 20, 'TRANS': 332} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1362 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "D" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1741 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1362 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "E" Number of atoms: 1731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 1731 Classifications: {'peptide': 351} Incomplete info: {'truncation_to_alanine': 309} Link IDs: {'PTRANS': 20, 'TRANS': 330} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1063 Unresolved non-hydrogen angles: 1358 Unresolved non-hydrogen dihedrals: 853 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Chain: "F" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 1741 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 311} Link IDs: {'PTRANS': 20, 'TRANS': 332} Unresolved chain link angles: 20 Unresolved non-hydrogen bonds: 1066 Unresolved non-hydrogen angles: 1362 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 117 Planarities with less than four sites: {'GLN:plan1': 21, 'HIS:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 15, 'ASP:plan': 17, 'PHE:plan': 11, 'GLU:plan': 22, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 533 Time building chain proxies: 6.44, per 1000 atoms: 0.62 Number of scatterers: 10426 At special positions: 0 Unit cell: (124.02, 121.9, 81.62, 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 2114 8.00 N 2114 7.00 C 6198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.96 Conformation dependent library (CDL) restraints added in 2.5 seconds 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3940 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 12 sheets defined 48.7% alpha, 21.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 1 through 14 Processing helix chain 'A' and resid 44 through 54 Processing helix chain 'A' and resid 57 through 68 Processing helix chain 'A' and resid 113 through 120 removed outlier: 4.210A pdb=" N ARG A 117 " --> pdb=" O PRO A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 152 Processing helix chain 'A' and resid 185 through 193 removed outlier: 3.520A pdb=" N TYR A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 197 removed outlier: 4.163A pdb=" N ASP A 197 " --> pdb=" O LEU A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 233 through 244 removed outlier: 3.775A pdb=" N VAL A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 260 Processing helix chain 'A' and resid 288 through 297 Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 302 through 309 Processing helix chain 'A' and resid 310 through 315 removed outlier: 3.543A pdb=" N PHE A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 Processing helix chain 'A' and resid 333 through 341 Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'B' and resid 2 through 14 Processing helix chain 'B' and resid 44 through 54 Processing helix chain 'B' and resid 57 through 68 Processing helix chain 'B' and resid 113 through 120 removed outlier: 4.142A pdb=" N ARG B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 152 Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.753A pdb=" N TYR B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) 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 208 through 221 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 249 through 260 Processing helix chain 'B' and resid 288 through 297 Processing helix chain 'B' and resid 302 through 309 Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 318 through 329 Processing helix chain 'B' and resid 333 through 341 Processing helix chain 'B' and resid 343 through 351 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 57 through 68 Processing helix chain 'C' and resid 113 through 120 removed outlier: 4.188A pdb=" N ARG C 117 " --> pdb=" O PRO C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 152 Processing helix chain 'C' and resid 185 through 193 Processing helix chain 'C' and resid 194 through 197 removed outlier: 4.067A pdb=" N ASP C 197 " --> pdb=" O LEU C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 246 through 248 No H-bonds generated for 'chain 'C' and resid 246 through 248' Processing helix chain 'C' and resid 249 through 260 Processing helix chain 'C' and resid 288 through 297 Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 302 through 310 Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 333 through 341 Processing helix chain 'C' and resid 343 through 353 Processing helix chain 'D' and resid 2 through 14 Processing helix chain 'D' and resid 44 through 54 Processing helix chain 'D' and resid 57 through 68 Processing helix chain 'D' and resid 113 through 120 removed outlier: 4.210A pdb=" N ARG D 117 " --> pdb=" O PRO D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 152 Processing helix chain 'D' and resid 185 through 193 removed outlier: 3.511A pdb=" N TYR D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 197 removed outlier: 4.167A pdb=" N ASP D 197 " --> pdb=" O LEU D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 194 through 197' Processing helix chain 'D' and resid 208 through 221 Processing helix chain 'D' and resid 233 through 244 removed outlier: 3.775A pdb=" N VAL D 244 " --> pdb=" O ARG D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 260 Processing helix chain 'D' and resid 288 through 297 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 302 through 309 Processing helix chain 'D' and resid 310 through 315 removed outlier: 3.542A pdb=" N PHE D 314 " --> pdb=" O GLY D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 329 Processing helix chain 'D' and resid 333 through 341 Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'E' and resid 2 through 14 Processing helix chain 'E' and resid 44 through 54 Processing helix chain 'E' and resid 57 through 68 Processing helix chain 'E' and resid 106 through 111 Processing helix chain 'E' and resid 113 through 120 removed outlier: 4.121A pdb=" N ARG E 117 " --> pdb=" O PRO E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 152 Processing helix chain 'E' and resid 185 through 193 removed outlier: 3.736A pdb=" N TYR E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 197 removed outlier: 4.025A pdb=" N ASP E 197 " --> pdb=" O LEU E 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 197' Processing helix chain 'E' and resid 208 through 221 Processing helix chain 'E' and resid 233 through 244 removed outlier: 3.547A pdb=" N VAL E 244 " --> pdb=" O ARG E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 248 No H-bonds generated for 'chain 'E' and resid 246 through 248' Processing helix chain 'E' and resid 249 through 260 Processing helix chain 'E' and resid 288 through 297 Processing helix chain 'E' and resid 302 through 309 Processing helix chain 'E' and resid 310 through 315 Processing helix chain 'E' and resid 318 through 329 Processing helix chain 'E' and resid 333 through 341 Processing helix chain 'E' and resid 343 through 351 Processing helix chain 'F' and resid 3 through 14 Processing helix chain 'F' and resid 44 through 54 Processing helix chain 'F' and resid 57 through 68 Processing helix chain 'F' and resid 113 through 120 removed outlier: 4.202A pdb=" N ARG F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 152 Processing helix chain 'F' and resid 185 through 193 Processing helix chain 'F' and resid 194 through 197 removed outlier: 4.091A pdb=" N ASP F 197 " --> pdb=" O LEU F 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 194 through 197' Processing helix chain 'F' and resid 208 through 221 Processing helix chain 'F' and resid 233 through 244 Processing helix chain 'F' and resid 249 through 260 Processing helix chain 'F' and resid 288 through 297 Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 302 through 310 Processing helix chain 'F' and resid 310 through 315 Processing helix chain 'F' and resid 318 through 329 Processing helix chain 'F' and resid 333 through 341 Processing helix chain 'F' and resid 343 through 353 removed outlier: 3.551A pdb=" N LEU F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 37 removed outlier: 3.653A pdb=" N GLN A 28 " --> pdb=" O HIS A 20 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG A 30 " --> pdb=" O ASP A 18 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP A 18 " --> pdb=" O ARG A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 173 through 178 removed outlier: 6.519A pdb=" N ILE A 156 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ARG A 177 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N THR A 158 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N HIS A 155 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU A 202 " --> pdb=" O HIS A 155 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 157 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLY A 204 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A 159 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 203 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N THR A 228 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLU A 205 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N CYS A 225 " --> pdb=" O GLY A 125 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 227 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU A 126 " --> pdb=" O GLY A 263 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU A 265 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU A 128 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN A 267 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR A 130 " --> pdb=" O GLN A 267 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N LEU A 269 " --> pdb=" O THR A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 34 through 37 removed outlier: 3.554A pdb=" N ASP B 18 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 173 through 178 removed outlier: 6.543A pdb=" N ILE B 156 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ARG B 177 " --> pdb=" O ILE B 156 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N THR B 158 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N HIS B 155 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 202 " --> pdb=" O HIS B 155 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL B 157 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLY B 204 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL B 159 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL B 201 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N THR B 228 " --> pdb=" O VAL B 201 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N VAL B 203 " --> pdb=" O THR B 228 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N CYS B 225 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL B 127 " --> pdb=" O CYS B 225 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N ALA B 227 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL B 129 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU B 229 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU B 126 " --> pdb=" O GLY B 263 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N LEU B 265 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU B 128 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLN B 267 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N THR B 130 " --> pdb=" O GLN B 267 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N LEU B 269 " --> pdb=" O THR B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 37 removed outlier: 3.718A pdb=" N ASP C 18 " --> pdb=" O ARG C 30 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 173 through 178 removed outlier: 6.242A pdb=" N VAL C 201 " --> pdb=" O PHE C 226 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N THR C 228 " --> pdb=" O VAL C 201 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N VAL C 203 " --> pdb=" O THR C 228 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 227 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 229 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU C 126 " --> pdb=" O GLY C 263 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU C 265 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU C 128 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N GLN C 267 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N THR C 130 " --> pdb=" O GLN C 267 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU C 269 " --> pdb=" O THR C 130 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 37 removed outlier: 3.646A pdb=" N GLN D 28 " --> pdb=" O HIS D 20 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG D 30 " --> pdb=" O ASP D 18 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP D 18 " --> pdb=" O ARG D 30 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 173 through 178 removed outlier: 6.518A pdb=" N ILE D 156 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ARG D 177 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N THR D 158 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS D 155 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU D 202 " --> pdb=" O HIS D 155 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N VAL D 157 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY D 204 " --> pdb=" O VAL D 157 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL D 159 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL D 203 " --> pdb=" O PHE D 226 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N THR D 228 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLU D 205 " --> pdb=" O THR D 228 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS D 225 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 227 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU D 126 " --> pdb=" O GLY D 263 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LEU D 265 " --> pdb=" O LEU D 126 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU D 128 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLN D 267 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N THR D 130 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N LEU D 269 " --> pdb=" O THR D 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 34 through 37 removed outlier: 3.631A pdb=" N ASP E 18 " --> pdb=" O ARG E 30 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 173 through 178 removed outlier: 6.524A pdb=" N ILE E 156 " --> pdb=" O ASN E 175 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ARG E 177 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N THR E 158 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS E 155 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU E 202 " --> pdb=" O HIS E 155 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL E 157 " --> pdb=" O LEU E 202 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY E 204 " --> pdb=" O VAL E 157 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N VAL E 159 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL E 201 " --> pdb=" O PHE E 226 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR E 228 " --> pdb=" O VAL E 201 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N VAL E 203 " --> pdb=" O THR E 228 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS E 225 " --> pdb=" O GLY E 125 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N VAL E 127 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA E 227 " --> pdb=" O VAL E 127 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL E 129 " --> pdb=" O ALA E 227 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU E 229 " --> pdb=" O VAL E 129 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 126 " --> pdb=" O GLY E 263 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU E 265 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU E 128 " --> pdb=" O LEU E 265 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N GLN E 267 " --> pdb=" O LEU E 128 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N THR E 130 " --> pdb=" O GLN E 267 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N LEU E 269 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 34 through 37 removed outlier: 3.745A pdb=" N ASP F 18 " --> pdb=" O ARG F 30 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 173 through 178 removed outlier: 6.208A pdb=" N VAL F 201 " --> pdb=" O PHE F 226 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR F 228 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N VAL F 203 " --> pdb=" O THR F 228 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA F 227 " --> pdb=" O VAL F 127 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU F 229 " --> pdb=" O VAL F 129 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU F 126 " --> pdb=" O GLY F 263 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU F 265 " --> pdb=" O LEU F 126 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N LEU F 128 " --> pdb=" O LEU F 265 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLN F 267 " --> pdb=" O LEU F 128 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR F 130 " --> pdb=" O GLN F 267 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N LEU F 269 " --> pdb=" O THR F 130 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2487 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: 3.65 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 2114 1.29 - 1.36: 2102 1.36 - 1.42: 4 1.42 - 1.49: 2112 1.49 - 1.55: 4088 Bond restraints: 10420 Sorted by residual: bond pdb=" C ALA E 2 " pdb=" O ALA E 2 " ideal model delta sigma weight residual 1.235 1.263 -0.028 1.26e-02 6.30e+03 5.00e+00 bond pdb=" CA ALA E 2 " pdb=" C ALA E 2 " ideal model delta sigma weight residual 1.523 1.546 -0.023 1.34e-02 5.57e+03 3.02e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 bond pdb=" N MET F 1 " pdb=" CA MET F 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.61e+00 ... (remaining 10415 not shown) Histogram of bond angle deviations from ideal: 96.56 - 103.50: 92 103.50 - 110.44: 2872 110.44 - 117.39: 4447 117.39 - 124.33: 6947 124.33 - 131.27: 134 Bond angle restraints: 14492 Sorted by residual: angle pdb=" C GLU F 160 " pdb=" N ASP F 161 " pdb=" CA ASP F 161 " ideal model delta sigma weight residual 122.56 130.62 -8.06 1.34e+00 5.57e-01 3.61e+01 angle pdb=" N ASP C 161 " pdb=" CA ASP C 161 " pdb=" C ASP C 161 " ideal model delta sigma weight residual 109.81 96.69 13.12 2.21e+00 2.05e-01 3.52e+01 angle pdb=" N LYS F 103 " pdb=" CA LYS F 103 " pdb=" C LYS F 103 " ideal model delta sigma weight residual 108.73 118.34 -9.61 1.63e+00 3.76e-01 3.47e+01 angle pdb=" N ASP F 161 " pdb=" CA ASP F 161 " pdb=" C ASP F 161 " ideal model delta sigma weight residual 107.91 96.56 11.35 2.05e+00 2.38e-01 3.07e+01 angle pdb=" N LYS C 103 " pdb=" CA LYS C 103 " pdb=" C LYS C 103 " ideal model delta sigma weight residual 109.24 118.08 -8.84 1.63e+00 3.76e-01 2.94e+01 ... (remaining 14487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.38: 6043 21.38 - 42.75: 1 42.75 - 64.13: 0 64.13 - 85.51: 0 85.51 - 106.88: 4 Dihedral angle restraints: 6048 sinusoidal: 0 harmonic: 6048 Sorted by residual: dihedral pdb=" CA ASP B 161 " pdb=" C ASP B 161 " pdb=" N PRO B 162 " pdb=" CA PRO B 162 " ideal model delta harmonic sigma weight residual -180.00 -73.12 -106.88 0 5.00e+00 4.00e-02 4.57e+02 dihedral pdb=" CA ASP E 161 " pdb=" C ASP E 161 " pdb=" N PRO E 162 " pdb=" CA PRO E 162 " ideal model delta harmonic sigma weight residual -180.00 -73.37 -106.63 0 5.00e+00 4.00e-02 4.55e+02 dihedral pdb=" CA ASP F 161 " pdb=" C ASP F 161 " pdb=" N PRO F 162 " pdb=" CA PRO F 162 " ideal model delta harmonic sigma weight residual -180.00 -84.19 -95.81 0 5.00e+00 4.00e-02 3.67e+02 ... (remaining 6045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1656 0.076 - 0.151: 284 0.151 - 0.227: 28 0.227 - 0.303: 0 0.303 - 0.378: 2 Chirality restraints: 1970 Sorted by residual: chirality pdb=" CA PRO B 162 " pdb=" N PRO B 162 " pdb=" C PRO B 162 " pdb=" CB PRO B 162 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" CA PRO E 162 " pdb=" N PRO E 162 " pdb=" C PRO E 162 " pdb=" CB PRO E 162 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA LEU F 294 " pdb=" N LEU F 294 " pdb=" C LEU F 294 " pdb=" CB LEU F 294 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1967 not shown) Planarity restraints: 2108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 2 " 0.022 2.00e-02 2.50e+03 4.40e-02 1.93e+01 pdb=" C ALA B 2 " -0.076 2.00e-02 2.50e+03 pdb=" O ALA B 2 " 0.027 2.00e-02 2.50e+03 pdb=" N ASN B 3 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 2 " -0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C ALA E 2 " 0.064 2.00e-02 2.50e+03 pdb=" O ALA E 2 " -0.023 2.00e-02 2.50e+03 pdb=" N ASN E 3 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 247 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C SER E 247 " -0.060 2.00e-02 2.50e+03 pdb=" O SER E 247 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR E 248 " 0.020 2.00e-02 2.50e+03 ... (remaining 2105 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 4456 2.90 - 3.40: 9964 3.40 - 3.90: 14393 3.90 - 4.40: 14662 4.40 - 4.90: 24269 Nonbonded interactions: 67744 Sorted by model distance: nonbonded pdb=" N ALA E 273 " pdb=" O HIS E 331 " model vdw 2.400 2.520 nonbonded pdb=" N ALA B 273 " pdb=" O HIS B 331 " model vdw 2.434 2.520 nonbonded pdb=" O GLU E 160 " pdb=" N VAL E 179 " model vdw 2.456 2.520 nonbonded pdb=" N THR A 130 " pdb=" O LEU A 265 " model vdw 2.464 2.520 nonbonded pdb=" O GLU B 160 " pdb=" N VAL B 179 " model vdw 2.465 2.520 ... (remaining 67739 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 351) selection = chain 'B' selection = (chain 'C' and resid 1 through 351) selection = (chain 'D' and resid 1 through 351) selection = chain 'E' selection = (chain 'F' and resid 1 through 351) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 3.980 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 32.280 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 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 : 0.004 0.086 10420 Z= 0.329 Angle : 1.052 13.117 14492 Z= 0.702 Chirality : 0.056 0.378 1970 Planarity : 0.005 0.044 2108 Dihedral : 6.943 106.883 2108 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.05 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 3.33 % 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: -0.51 (0.17), residues: 2102 helix: -0.57 (0.14), residues: 990 sheet: 0.99 (0.25), residues: 456 loop : -0.66 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.081 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0918 time to fit residues: 12.8160 Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 88 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 164 optimal weight: 50.0000 chunk 63 optimal weight: 10.0000 chunk 100 optimal weight: 0.0970 chunk 122 optimal weight: 20.0000 chunk 190 optimal weight: 5.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5982 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10420 Z= 0.201 Angle : 0.585 8.309 14492 Z= 0.373 Chirality : 0.046 0.180 1970 Planarity : 0.004 0.024 2108 Dihedral : 5.939 47.770 2108 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.28 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.67 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.10 % 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: 0.12 (0.18), residues: 2102 helix: 0.22 (0.16), residues: 998 sheet: 0.79 (0.26), residues: 460 loop : -0.44 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE A 64 TYR 0.000 0.000 TYR A 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4204 Ramachandran restraints generated. 2102 Oldfield, 0 Emsley, 2102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.125 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0901 time to fit residues: 12.6898 Evaluate side-chains 66 residues out of total 1862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 64.3427 > 50: distance: 2 - 16: 11.513 distance: 6 - 21: 25.275 distance: 10 - 26: 26.565 distance: 13 - 16: 13.805 distance: 14 - 31: 24.133 distance: 16 - 17: 14.909 distance: 17 - 18: 5.827 distance: 17 - 20: 11.532 distance: 18 - 19: 26.242 distance: 18 - 21: 20.430 distance: 21 - 22: 28.768 distance: 22 - 23: 21.683 distance: 22 - 25: 20.147 distance: 23 - 24: 23.073 distance: 23 - 26: 22.950 distance: 26 - 27: 28.451 distance: 27 - 28: 19.864 distance: 27 - 30: 20.293 distance: 28 - 29: 31.598 distance: 28 - 31: 21.954 distance: 31 - 32: 4.671 distance: 32 - 33: 15.182 distance: 32 - 35: 18.653 distance: 33 - 34: 17.682 distance: 33 - 36: 25.291 distance: 36 - 37: 43.040 distance: 37 - 38: 50.894 distance: 37 - 40: 11.571 distance: 38 - 39: 34.342 distance: 38 - 41: 32.957 distance: 41 - 42: 32.291 distance: 42 - 43: 30.271 distance: 43 - 44: 47.191 distance: 43 - 46: 30.835 distance: 46 - 47: 10.648 distance: 47 - 48: 16.532 distance: 47 - 50: 5.175 distance: 48 - 49: 5.702 distance: 48 - 51: 24.035 distance: 51 - 52: 25.791 distance: 52 - 53: 11.380 distance: 52 - 55: 19.250 distance: 53 - 54: 16.873 distance: 53 - 56: 13.252 distance: 56 - 57: 20.240 distance: 57 - 58: 38.844 distance: 57 - 60: 3.677 distance: 58 - 59: 35.843 distance: 58 - 61: 7.520 distance: 61 - 62: 32.766 distance: 62 - 63: 17.228 distance: 62 - 65: 35.300 distance: 63 - 64: 51.218 distance: 63 - 66: 26.231 distance: 64 - 81: 34.947