Starting phenix.real_space_refine on Sat Aug 3 23:28:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lbh_0869/08_2024/6lbh_0869.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lbh_0869/08_2024/6lbh_0869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lbh_0869/08_2024/6lbh_0869.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lbh_0869/08_2024/6lbh_0869.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lbh_0869/08_2024/6lbh_0869.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lbh_0869/08_2024/6lbh_0869.cif" } resolution = 3.7 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= 0.003 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 34 5.16 5 C 5907 2.51 5 N 1507 2.21 5 O 1771 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 418": "OD1" <-> "OD2" Residue "A ARG 444": "NH1" <-> "NH2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 311": "OE1" <-> "OE2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ASP 346": "OD1" <-> "OD2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B ASP 351": "OD1" <-> "OD2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B TYR 379": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 381": "OD1" <-> "OD2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 418": "OD1" <-> "OD2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "D ASP 33": "OD1" <-> "OD2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 156": "OD1" <-> "OD2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D ASP 175": "OD1" <-> "OD2" Residue "D TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 189": "OD1" <-> "OD2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 222": "OE1" <-> "OE2" Residue "F ASP 33": "OD1" <-> "OD2" Residue "F TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 156": "OD1" <-> "OD2" Residue "F TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 189": "OD1" <-> "OD2" Residue "F TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 74": "NH1" <-> "NH2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9219 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1352 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 170} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1356 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 170} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1618 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 204} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "C" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1637 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "F" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1612 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 204} Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 54 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Chain: "E" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1644 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 212} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 5.66, per 1000 atoms: 0.61 Number of scatterers: 9219 At special positions: 0 Unit cell: (113.98, 122.18, 125.46, 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 34 16.00 O 1771 8.00 N 1507 7.00 C 5907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 93 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 199 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 206 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 93 " distance=2.04 Simple disulfide: pdb=" SG CYS F 139 " - pdb=" SG CYS F 199 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 206 " distance=2.03 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: 3.65 Conformation dependent library (CDL) restraints added in 1.7 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2276 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 22 sheets defined 30.7% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 277 through 306 removed outlier: 4.020A pdb=" N ALA A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 295 " --> pdb=" O ILE A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 311 removed outlier: 3.855A pdb=" N LEU A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 318 Processing helix chain 'A' and resid 319 through 343 removed outlier: 4.230A pdb=" N ASN A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASN A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 351 through 382 removed outlier: 3.879A pdb=" N LEU A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 358 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 416 removed outlier: 3.755A pdb=" N VAL A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A 400 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Proline residue: A 409 - end of helix Processing helix chain 'A' and resid 418 through 423 removed outlier: 3.920A pdb=" N VAL A 422 " --> pdb=" O ASP A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.717A pdb=" N ALA A 428 " --> pdb=" O ASN A 424 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 306 removed outlier: 4.376A pdb=" N ILE B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 306 " --> pdb=" O ILE B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.587A pdb=" N LEU B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 318 Processing helix chain 'B' and resid 319 through 344 removed outlier: 3.572A pdb=" N ASN B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 341 " --> pdb=" O LEU B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 382 removed outlier: 3.744A pdb=" N VAL B 355 " --> pdb=" O ASP B 351 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR B 369 " --> pdb=" O LEU B 365 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 401 removed outlier: 3.699A pdb=" N VAL B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 416 Proline residue: B 409 - end of helix Processing helix chain 'B' and resid 423 through 433 removed outlier: 3.748A pdb=" N ALA B 428 " --> pdb=" O ASN B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 438 through 447 Processing helix chain 'D' and resid 126 through 131 removed outlier: 3.691A pdb=" N THR D 131 " --> pdb=" O SER D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 194 removed outlier: 3.661A pdb=" N HIS D 194 " --> pdb=" O GLU D 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 30 No H-bonds generated for 'chain 'C' and resid 28 through 30' Processing helix chain 'C' and resid 61 through 65 removed outlier: 3.625A pdb=" N LYS C 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'F' and resid 126 through 131 removed outlier: 3.639A pdb=" N THR F 131 " --> pdb=" O SER F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 194 removed outlier: 3.625A pdb=" N HIS F 194 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 61 through 65 removed outlier: 3.670A pdb=" N LYS E 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.531A pdb=" N SER E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 5 through 7 removed outlier: 3.585A pdb=" N THR D 5 " --> pdb=" O ARG D 24 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR D 7 " --> pdb=" O SER D 22 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP D 75 " --> pdb=" O SER D 72 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 72 " --> pdb=" O ASP D 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 13 removed outlier: 6.029A pdb=" N GLU D 110 " --> pdb=" O VAL D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 50 through 53 removed outlier: 5.455A pdb=" N LEU D 51 " --> pdb=" O LEU D 42 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N LEU D 42 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 119 through 123 removed outlier: 3.665A pdb=" N ASN D 142 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N TYR D 178 " --> pdb=" O ASN D 143 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 165 " --> pdb=" O THR D 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 158 through 159 Processing sheet with id=AA6, first strand: chain 'C' and resid 5 through 6 removed outlier: 3.729A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.698A pdb=" N ILE C 121 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASN C 33 " --> pdb=" O GLY C 99 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N TRP C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.698A pdb=" N ILE C 121 " --> pdb=" O GLU C 10 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.550A pdb=" N SER C 131 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR C 186 " --> pdb=" O GLY C 155 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.550A pdb=" N SER C 131 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR C 186 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 180 " --> pdb=" O THR C 187 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 165 removed outlier: 3.607A pdb=" N THR C 162 " --> pdb=" O ALA C 209 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN C 207 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.569A pdb=" N THR F 5 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP F 75 " --> pdb=" O SER F 72 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER F 72 " --> pdb=" O ASP F 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 12 through 13 removed outlier: 5.959A pdb=" N GLU F 110 " --> pdb=" O VAL F 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 50 through 53 removed outlier: 5.429A pdb=" N LEU F 51 " --> pdb=" O LEU F 42 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N LEU F 42 " --> pdb=" O LEU F 51 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 119 through 123 removed outlier: 3.764A pdb=" N ASN F 142 " --> pdb=" O THR F 119 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR F 178 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU F 165 " --> pdb=" O THR F 183 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 158 through 159 Processing sheet with id=AB8, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.727A pdb=" N THR E 78 " --> pdb=" O ASP E 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.570A pdb=" N ILE E 121 " --> pdb=" O GLU E 10 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN E 33 " --> pdb=" O GLY E 99 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.570A pdb=" N ILE E 121 " --> pdb=" O GLU E 10 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AC3, first strand: chain 'E' and resid 131 through 133 removed outlier: 3.690A pdb=" N VAL E 180 " --> pdb=" O THR E 187 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 162 through 165 removed outlier: 3.522A pdb=" N THR E 162 " --> pdb=" O ALA E 209 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 4.01 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: 2896 1.34 - 1.46: 2284 1.46 - 1.58: 4205 1.58 - 1.70: 0 1.70 - 1.81: 50 Bond restraints: 9435 Sorted by residual: bond pdb=" CB VAL B 398 " pdb=" CG2 VAL B 398 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.49e+00 bond pdb=" N TYR E 109E" pdb=" CA TYR E 109E" ideal model delta sigma weight residual 1.459 1.446 0.013 9.10e-03 1.21e+04 2.06e+00 bond pdb=" CG1 ILE B 339 " pdb=" CD1 ILE B 339 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.03e+00 bond pdb=" N TYR C 109E" pdb=" CA TYR C 109E" ideal model delta sigma weight residual 1.459 1.447 0.012 9.10e-03 1.21e+04 1.85e+00 bond pdb=" CB VAL E 37 " pdb=" CG1 VAL E 37 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 ... (remaining 9430 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.25: 189 105.25 - 112.45: 5076 112.45 - 119.64: 2945 119.64 - 126.83: 4550 126.83 - 134.03: 148 Bond angle restraints: 12908 Sorted by residual: angle pdb=" N MET E 111G" pdb=" CA MET E 111G" pdb=" C MET E 111G" ideal model delta sigma weight residual 110.06 117.32 -7.26 1.43e+00 4.89e-01 2.58e+01 angle pdb=" N ALA C 110F" pdb=" CA ALA C 110F" pdb=" C ALA C 110F" ideal model delta sigma weight residual 111.34 118.66 -7.32 1.49e+00 4.50e-01 2.42e+01 angle pdb=" N ALA E 110F" pdb=" CA ALA E 110F" pdb=" C ALA E 110F" ideal model delta sigma weight residual 112.12 118.67 -6.55 1.34e+00 5.57e-01 2.39e+01 angle pdb=" C TYR C 109E" pdb=" N ALA C 110F" pdb=" CA ALA C 110F" ideal model delta sigma weight residual 121.90 116.05 5.85 1.26e+00 6.30e-01 2.15e+01 angle pdb=" N MET C 111G" pdb=" CA MET C 111G" pdb=" C MET C 111G" ideal model delta sigma weight residual 109.83 116.94 -7.11 1.55e+00 4.16e-01 2.10e+01 ... (remaining 12903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 5008 17.34 - 34.69: 418 34.69 - 52.03: 88 52.03 - 69.37: 7 69.37 - 86.72: 7 Dihedral angle restraints: 5528 sinusoidal: 1968 harmonic: 3560 Sorted by residual: dihedral pdb=" CA LYS F 55 " pdb=" C LYS F 55 " pdb=" N VAL F 56 " pdb=" CA VAL F 56 " ideal model delta harmonic sigma weight residual -180.00 -139.17 -40.83 0 5.00e+00 4.00e-02 6.67e+01 dihedral pdb=" CA LYS D 55 " pdb=" C LYS D 55 " pdb=" N VAL D 56 " pdb=" CA VAL D 56 " ideal model delta harmonic sigma weight residual -180.00 -139.69 -40.31 0 5.00e+00 4.00e-02 6.50e+01 dihedral pdb=" CA ASN D 35E" pdb=" C ASN D 35E" pdb=" N THR D 36 " pdb=" CA THR D 36 " ideal model delta harmonic sigma weight residual 180.00 141.92 38.08 0 5.00e+00 4.00e-02 5.80e+01 ... (remaining 5525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 956 0.037 - 0.073: 414 0.073 - 0.110: 131 0.110 - 0.147: 32 0.147 - 0.183: 6 Chirality restraints: 1539 Sorted by residual: chirality pdb=" CA THR F 36 " pdb=" N THR F 36 " pdb=" C THR F 36 " pdb=" CB THR F 36 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA THR D 36 " pdb=" N THR D 36 " pdb=" C THR D 36 " pdb=" CB THR D 36 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.34e-01 chirality pdb=" CA ALA E 110F" pdb=" N ALA E 110F" pdb=" C ALA E 110F" pdb=" CB ALA E 110F" both_signs ideal model delta sigma weight residual False 2.48 2.31 0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1536 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 331 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C GLY B 331 " 0.043 2.00e-02 2.50e+03 pdb=" O GLY B 331 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B 332 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 331 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C GLY A 331 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY A 331 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN A 332 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR D 145 " 0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO D 146 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " 0.020 5.00e-02 4.00e+02 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 179 2.64 - 3.21: 9089 3.21 - 3.77: 14396 3.77 - 4.34: 20067 4.34 - 4.90: 33017 Nonbonded interactions: 76748 Sorted by model distance: nonbonded pdb=" O GLN F 129 " pdb=" NZ LYS F 188 " model vdw 2.079 3.120 nonbonded pdb=" OH TYR A 273 " pdb=" OE2 GLU B 359 " model vdw 2.143 3.040 nonbonded pdb=" OD1 ASN F 150 " pdb=" OG1 THR F 202 " model vdw 2.161 3.040 nonbonded pdb=" OE2 GLU A 359 " pdb=" OH TYR B 273 " model vdw 2.161 3.040 nonbonded pdb=" OD1 ASN D 150 " pdb=" OG1 THR D 202 " model vdw 2.171 3.040 ... (remaining 76743 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' and (resid 271 through 339 or (resid 340 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD )) or resid 341 through 448)) } ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 1 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 121 or (resid 122 through 126 and ( \ name N or name CA or name C or name O or name CB )) or resid 127 through 224)) } ncs_group { reference = (chain 'D' and (resid 1 through 112 or (resid 113 through 114 and (name N or nam \ e CA or name C or name O or name CB )) or resid 115 through 216)) selection = chain 'F' } 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: 1.930 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.580 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 9435 Z= 0.380 Angle : 0.825 8.217 12908 Z= 0.450 Chirality : 0.046 0.183 1539 Planarity : 0.005 0.040 1612 Dihedral : 13.616 86.716 3228 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.68 % Favored : 92.16 % Rotamer: Outliers : 0.20 % Allowed : 0.10 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.87 (0.23), residues: 1224 helix: -1.18 (0.29), residues: 310 sheet: -2.12 (0.23), residues: 418 loop : -1.95 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.011 0.001 HIS F 39 PHE 0.024 0.002 PHE E 177 TYR 0.026 0.002 TYR E 133 ARG 0.006 0.001 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 253 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 LYS cc_start: 0.8128 (tppt) cc_final: 0.7892 (mmmt) REVERT: F 188 LYS cc_start: 0.6456 (mmtt) cc_final: 0.6156 (mmtt) REVERT: E 109 TYR cc_start: 0.7789 (t80) cc_final: 0.7515 (t80) outliers start: 2 outliers final: 0 residues processed: 253 average time/residue: 0.2008 time to fit residues: 70.7747 Evaluate side-chains 215 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 6 GLN D 58 ASN ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 194 HIS F 6 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 GLN F 58 ASN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 194 HIS E 39 GLN E 104 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9435 Z= 0.229 Angle : 0.703 9.674 12908 Z= 0.361 Chirality : 0.045 0.171 1539 Planarity : 0.005 0.036 1612 Dihedral : 5.626 43.405 1322 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.28 % Allowed : 11.72 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -2.52 (0.24), residues: 1224 helix: -1.05 (0.28), residues: 328 sheet: -1.84 (0.25), residues: 390 loop : -1.75 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 288 HIS 0.003 0.001 HIS F 39 PHE 0.013 0.001 PHE E 177 TYR 0.015 0.001 TYR E 109E ARG 0.005 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 248 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7481 (tm-30) REVERT: B 297 MET cc_start: 0.6810 (ttp) cc_final: 0.6553 (ttm) REVERT: D 128 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7515 (tm-30) REVERT: D 180 MET cc_start: 0.7481 (ttt) cc_final: 0.7270 (ttt) REVERT: F 172 ASP cc_start: 0.7034 (t70) cc_final: 0.6630 (t0) REVERT: F 175 ASP cc_start: 0.7993 (p0) cc_final: 0.7629 (p0) outliers start: 23 outliers final: 15 residues processed: 255 average time/residue: 0.2012 time to fit residues: 71.6672 Evaluate side-chains 245 residues out of total 1070 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 230 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 38 LEU Chi-restraints excluded: chain F residue 50 LYS Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 164 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- 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: 53.7878 > 50: distance: 88 - 193: 22.328 distance: 91 - 190: 11.565 distance: 134 - 139: 9.009 distance: 139 - 140: 19.255 distance: 139 - 145: 12.368 distance: 140 - 141: 17.303 distance: 140 - 143: 33.356 distance: 141 - 142: 33.975 distance: 141 - 146: 13.251 distance: 143 - 144: 20.762 distance: 144 - 145: 26.270 distance: 146 - 147: 28.890 distance: 147 - 148: 6.713 distance: 147 - 150: 23.338 distance: 148 - 149: 14.787 distance: 148 - 160: 13.162 distance: 150 - 151: 3.871 distance: 151 - 152: 10.078 distance: 151 - 153: 7.567 distance: 152 - 154: 6.745 distance: 153 - 155: 12.311 distance: 153 - 156: 8.612 distance: 154 - 155: 8.533 distance: 155 - 157: 8.000 distance: 156 - 158: 8.552 distance: 157 - 159: 12.716 distance: 158 - 159: 8.874 distance: 160 - 161: 7.194 distance: 161 - 162: 12.611 distance: 161 - 164: 10.373 distance: 162 - 163: 13.120 distance: 162 - 167: 6.297 distance: 164 - 165: 17.086 distance: 164 - 166: 5.565 distance: 167 - 168: 17.202 distance: 168 - 169: 8.790 distance: 168 - 171: 24.891 distance: 169 - 170: 28.113 distance: 169 - 178: 18.620 distance: 171 - 172: 10.248 distance: 172 - 173: 19.038 distance: 172 - 174: 6.390 distance: 173 - 175: 5.351 distance: 174 - 176: 8.196 distance: 175 - 177: 12.032 distance: 176 - 177: 15.190 distance: 178 - 179: 19.101 distance: 179 - 180: 22.422 distance: 180 - 181: 15.972 distance: 180 - 182: 20.221 distance: 182 - 183: 23.119 distance: 184 - 185: 20.413 distance: 184 - 186: 28.155 distance: 186 - 187: 14.980 distance: 187 - 188: 27.407 distance: 188 - 189: 20.261 distance: 188 - 190: 14.582 distance: 190 - 191: 8.772 distance: 191 - 192: 13.240 distance: 191 - 194: 18.521 distance: 192 - 193: 7.438 distance: 192 - 197: 4.213 distance: 194 - 195: 14.512 distance: 194 - 196: 10.592 distance: 197 - 198: 4.119 distance: 198 - 199: 20.454 distance: 198 - 201: 10.575 distance: 199 - 200: 4.607 distance: 199 - 202: 20.154 distance: 202 - 203: 13.891 distance: 203 - 204: 27.535 distance: 203 - 206: 8.360 distance: 204 - 205: 8.539 distance: 204 - 210: 27.425 distance: 206 - 207: 9.035 distance: 207 - 208: 7.952 distance: 207 - 209: 13.503