Starting phenix.real_space_refine on Tue Nov 14 19:32:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/11_2023/6x2l_22011.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/11_2023/6x2l_22011.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/11_2023/6x2l_22011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/11_2023/6x2l_22011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/11_2023/6x2l_22011.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x2l_22011/11_2023/6x2l_22011.pdb" } resolution = 2.85 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 6159 2.51 5 N 1491 2.21 5 O 1677 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 39": "NH1" <-> "NH2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A ARG 353": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ASP 444": "OD1" <-> "OD2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "B ARG 39": "NH1" <-> "NH2" Residue "B GLU 40": "OE1" <-> "OE2" Residue "B PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ASP 275": "OD1" <-> "OD2" Residue "B ARG 353": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ASP 444": "OD1" <-> "OD2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 272": "OE1" <-> "OE2" Residue "C ASP 275": "OD1" <-> "OD2" Residue "C ARG 353": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ASP 444": "OD1" <-> "OD2" Residue "C ARG 447": "NH1" <-> "NH2" Residue "C PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 471": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 9396 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Chain: "B" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Chain: "C" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Time building chain proxies: 5.42, per 1000 atoms: 0.58 Number of scatterers: 9396 At special positions: 0 Unit cell: (113.984, 109.824, 82.368, 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 69 16.00 O 1677 8.00 N 1491 7.00 C 6159 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: 3.36 Conformation dependent library (CDL) restraints added in 1.8 seconds 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 6 sheets defined 81.3% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 21 through 40 removed outlier: 3.613A pdb=" N ALA A 27 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 53 removed outlier: 3.739A pdb=" N ALA A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 86 removed outlier: 3.580A pdb=" N LEU A 59 " --> pdb=" O PRO A 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.761A pdb=" N SER A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 117 removed outlier: 3.565A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.554A pdb=" N MET A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 230 removed outlier: 3.517A pdb=" N GLY A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 273 Proline residue: A 259 - end of helix removed outlier: 3.631A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 299 removed outlier: 3.679A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.623A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 319 removed outlier: 3.608A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 removed outlier: 3.548A pdb=" N THR A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 349 removed outlier: 4.158A pdb=" N ARG A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 removed outlier: 4.179A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.595A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 401 removed outlier: 3.696A pdb=" N THR A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 406 removed outlier: 3.527A pdb=" N SER A 405 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 427 removed outlier: 3.592A pdb=" N MET A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.995A pdb=" N ILE A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 466 removed outlier: 3.594A pdb=" N LEU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG A 445 " --> pdb=" O TRP A 441 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.613A pdb=" N ALA B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.739A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 86 removed outlier: 3.580A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 3.761A pdb=" N SER B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 117 removed outlier: 3.565A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.554A pdb=" N MET B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 230 removed outlier: 3.518A pdb=" N GLY B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 Proline residue: B 259 - end of helix removed outlier: 3.631A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 299 removed outlier: 3.679A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.624A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.608A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 removed outlier: 3.549A pdb=" N THR B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 349 removed outlier: 4.158A pdb=" N ARG B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 removed outlier: 4.179A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Proline residue: B 360 - end of helix Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.595A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 401 removed outlier: 3.696A pdb=" N THR B 396 " --> pdb=" O GLY B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 406 removed outlier: 3.528A pdb=" N SER B 405 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 427 removed outlier: 3.592A pdb=" N MET B 419 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.994A pdb=" N ILE B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.595A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 40 removed outlier: 3.613A pdb=" N ALA C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.739A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 86 removed outlier: 3.579A pdb=" N LEU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix removed outlier: 3.762A pdb=" N SER C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 117 removed outlier: 3.565A pdb=" N VAL C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.555A pdb=" N MET C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 230 removed outlier: 3.518A pdb=" N GLY C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 Proline residue: C 259 - end of helix removed outlier: 3.631A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 299 removed outlier: 3.678A pdb=" N THR C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.622A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 319 removed outlier: 3.608A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 removed outlier: 3.548A pdb=" N THR C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 349 removed outlier: 4.158A pdb=" N ARG C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASN C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 363 removed outlier: 4.179A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Proline residue: C 360 - end of helix Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.595A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.696A pdb=" N THR C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 406 removed outlier: 3.527A pdb=" N SER C 405 " --> pdb=" O THR C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 427 removed outlier: 3.592A pdb=" N MET C 419 " --> pdb=" O GLY C 415 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 432 removed outlier: 3.589A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.594A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG C 445 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N MET C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 167 Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA4, first strand: chain 'B' and resid 164 through 167 Processing sheet with id=AA5, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AA6, first strand: chain 'C' and resid 164 through 167 624 hydrogen bonds defined for protein. 1836 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: 2.66 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1670 1.32 - 1.45: 2168 1.45 - 1.57: 5573 1.57 - 1.70: 0 1.70 - 1.82: 123 Bond restraints: 9534 Sorted by residual: bond pdb=" C MET C 419 " pdb=" O MET C 419 " ideal model delta sigma weight residual 1.237 1.200 0.037 1.19e-02 7.06e+03 9.55e+00 bond pdb=" C MET A 419 " pdb=" O MET A 419 " ideal model delta sigma weight residual 1.237 1.200 0.036 1.19e-02 7.06e+03 9.28e+00 bond pdb=" C MET B 419 " pdb=" O MET B 419 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.19e-02 7.06e+03 9.09e+00 bond pdb=" N LEU B 372 " pdb=" CA LEU B 372 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.41e+00 bond pdb=" N LEU A 372 " pdb=" CA LEU A 372 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.20e+00 ... (remaining 9529 not shown) Histogram of bond angle deviations from ideal: 97.94 - 105.14: 171 105.14 - 112.34: 4890 112.34 - 119.54: 3415 119.54 - 126.73: 4391 126.73 - 133.93: 69 Bond angle restraints: 12936 Sorted by residual: angle pdb=" C ASP C 388 " pdb=" N LEU C 389 " pdb=" CA LEU C 389 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" C ASP A 388 " pdb=" N LEU A 389 " pdb=" CA LEU A 389 " ideal model delta sigma weight residual 121.54 128.87 -7.33 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C ASP B 388 " pdb=" N LEU B 389 " pdb=" CA LEU B 389 " ideal model delta sigma weight residual 121.54 128.84 -7.30 1.91e+00 2.74e-01 1.46e+01 angle pdb=" CB MET C 473 " pdb=" CG MET C 473 " pdb=" SD MET C 473 " ideal model delta sigma weight residual 112.70 103.26 9.44 3.00e+00 1.11e-01 9.89e+00 angle pdb=" CB MET A 473 " pdb=" CG MET A 473 " pdb=" SD MET A 473 " ideal model delta sigma weight residual 112.70 103.30 9.40 3.00e+00 1.11e-01 9.82e+00 ... (remaining 12931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 5150 16.78 - 33.56: 430 33.56 - 50.35: 96 50.35 - 67.13: 21 67.13 - 83.91: 9 Dihedral angle restraints: 5706 sinusoidal: 2172 harmonic: 3534 Sorted by residual: dihedral pdb=" CA LEU A 384 " pdb=" C LEU A 384 " pdb=" N ASN A 385 " pdb=" CA ASN A 385 " ideal model delta harmonic sigma weight residual 180.00 160.52 19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU C 384 " pdb=" C LEU C 384 " pdb=" N ASN C 385 " pdb=" CA ASN C 385 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA LEU B 384 " pdb=" C LEU B 384 " pdb=" N ASN B 385 " pdb=" CA ASN B 385 " ideal model delta harmonic sigma weight residual 180.00 160.54 19.46 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 847 0.039 - 0.077: 565 0.077 - 0.116: 154 0.116 - 0.154: 59 0.154 - 0.193: 19 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CB VAL C 433 " pdb=" CA VAL C 433 " pdb=" CG1 VAL C 433 " pdb=" CG2 VAL C 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CB VAL B 433 " pdb=" CA VAL B 433 " pdb=" CG1 VAL B 433 " pdb=" CG2 VAL B 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CB VAL A 433 " pdb=" CA VAL A 433 " pdb=" CG1 VAL A 433 " pdb=" CG2 VAL A 433 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 1641 not shown) Planarity restraints: 1572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 301 " -0.049 5.00e-02 4.00e+02 7.26e-02 8.43e+00 pdb=" N PRO C 302 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 301 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO B 302 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 302 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 302 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.049 5.00e-02 4.00e+02 7.25e-02 8.40e+00 pdb=" N PRO A 302 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.041 5.00e-02 4.00e+02 ... (remaining 1569 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 60 2.64 - 3.21: 8450 3.21 - 3.77: 14468 3.77 - 4.34: 20729 4.34 - 4.90: 33676 Nonbonded interactions: 77383 Sorted by model distance: nonbonded pdb=" N GLN B 413 " pdb=" OE1 GLN B 413 " model vdw 2.078 2.520 nonbonded pdb=" N GLN A 413 " pdb=" OE1 GLN A 413 " model vdw 2.079 2.520 nonbonded pdb=" N GLN C 413 " pdb=" OE1 GLN C 413 " model vdw 2.079 2.520 nonbonded pdb=" O SER A 331 " pdb=" OG SER A 331 " model vdw 2.339 2.440 nonbonded pdb=" O SER B 331 " pdb=" OG SER B 331 " model vdw 2.339 2.440 ... (remaining 77378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.130 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: 5.550 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 27.640 Find NCS groups from input model: 0.530 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:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 : 0.009 0.075 9534 Z= 0.585 Angle : 0.960 9.435 12936 Z= 0.513 Chirality : 0.056 0.193 1644 Planarity : 0.007 0.073 1572 Dihedral : 13.682 83.912 3426 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.46 (0.14), residues: 1215 helix: -4.23 (0.07), residues: 975 sheet: -2.87 (0.80), residues: 54 loop : -2.72 (0.35), residues: 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.100 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 200 average time/residue: 1.2676 time to fit residues: 270.5347 Evaluate side-chains 147 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 145 time to evaluate : 1.072 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1294 time to fit residues: 1.8768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.7980 chunk 93 optimal weight: 0.0870 chunk 51 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 62 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 chunk 37 optimal weight: 0.0170 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 85 ASN C 85 ASN C 156 GLN C 322 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9534 Z= 0.150 Angle : 0.550 8.112 12936 Z= 0.287 Chirality : 0.038 0.124 1644 Planarity : 0.005 0.037 1572 Dihedral : 4.501 17.724 1293 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.03 % Allowed : 10.05 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.20), residues: 1215 helix: -1.57 (0.14), residues: 957 sheet: -2.87 (0.72), residues: 54 loop : -2.31 (0.37), residues: 204 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.058 Fit side-chains outliers start: 21 outliers final: 7 residues processed: 179 average time/residue: 1.1220 time to fit residues: 216.1021 Evaluate side-chains 151 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 0.2928 time to fit residues: 3.2965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 156 GLN B 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9534 Z= 0.238 Angle : 0.546 6.963 12936 Z= 0.281 Chirality : 0.040 0.124 1644 Planarity : 0.004 0.035 1572 Dihedral : 4.237 18.550 1293 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.71 % Allowed : 13.33 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.23), residues: 1215 helix: -0.23 (0.16), residues: 966 sheet: -2.48 (0.73), residues: 54 loop : -2.45 (0.39), residues: 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 0.963 Fit side-chains outliers start: 28 outliers final: 14 residues processed: 171 average time/residue: 1.1768 time to fit residues: 216.2550 Evaluate side-chains 157 residues out of total 1035 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 0.984 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 6 residues processed: 8 average time/residue: 0.2574 time to fit residues: 3.9736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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-1.21rc1-5144/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: 70.7217 > 50: distance: 63 - 82: 20.090 distance: 69 - 90: 36.910 distance: 74 - 96: 22.746 distance: 77 - 82: 23.220 distance: 82 - 83: 34.728 distance: 83 - 84: 38.137 distance: 83 - 86: 7.160 distance: 84 - 85: 25.838 distance: 84 - 90: 39.157 distance: 85 - 108: 53.267 distance: 86 - 87: 23.393 distance: 87 - 88: 7.531 distance: 87 - 89: 28.410 distance: 90 - 91: 7.742 distance: 91 - 92: 40.877 distance: 91 - 94: 31.608 distance: 92 - 96: 43.603 distance: 94 - 95: 38.978 distance: 96 - 97: 7.726 distance: 97 - 98: 56.040 distance: 97 - 100: 15.074 distance: 98 - 99: 39.400 distance: 98 - 101: 11.979 distance: 101 - 102: 36.032 distance: 102 - 103: 17.041 distance: 102 - 105: 28.402 distance: 103 - 104: 26.237 distance: 103 - 108: 19.761 distance: 105 - 106: 7.151 distance: 105 - 107: 22.429 distance: 108 - 109: 57.514 distance: 110 - 111: 30.238 distance: 110 - 112: 48.903 distance: 113 - 114: 29.218 distance: 114 - 115: 28.404 distance: 114 - 120: 22.915 distance: 116 - 117: 30.940 distance: 117 - 118: 36.364 distance: 117 - 119: 19.990 distance: 120 - 121: 21.139 distance: 120 - 126: 25.692 distance: 121 - 122: 47.140 distance: 121 - 124: 50.125 distance: 122 - 123: 7.822 distance: 122 - 127: 34.875 distance: 124 - 125: 20.172 distance: 125 - 126: 21.132 distance: 127 - 128: 26.026 distance: 128 - 129: 40.558 distance: 128 - 131: 9.235 distance: 129 - 132: 4.392 distance: 132 - 133: 37.640 distance: 133 - 134: 28.809 distance: 133 - 136: 40.474 distance: 134 - 135: 17.795 distance: 134 - 141: 16.381 distance: 136 - 137: 17.117 distance: 137 - 138: 6.417 distance: 138 - 139: 57.319 distance: 138 - 140: 36.126 distance: 141 - 142: 14.279 distance: 142 - 143: 13.603 distance: 142 - 145: 17.473 distance: 143 - 144: 15.658 distance: 143 - 149: 19.331 distance: 145 - 146: 24.653 distance: 146 - 147: 53.743 distance: 146 - 148: 38.435