Starting phenix.real_space_refine on Sat Jan 20 12:13:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/01_2024/6hup_0283_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/01_2024/6hup_0283.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/01_2024/6hup_0283_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/01_2024/6hup_0283_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/01_2024/6hup_0283_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/01_2024/6hup_0283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/01_2024/6hup_0283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/01_2024/6hup_0283_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hup_0283/01_2024/6hup_0283_updated.pdb" } resolution = 3.58 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 83 5.16 5 Cl 3 4.86 5 C 9878 2.51 5 N 2477 2.21 5 O 2818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "C ARG 324": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 180": "NH1" <-> "NH2" Residue "E ARG 269": "NH1" <-> "NH2" Residue "G PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 15265 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2786 Classifications: {'peptide': 344} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 329} Chain breaks: 1 Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2758 Classifications: {'peptide': 336} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2720 Classifications: {'peptide': 330} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 316} Chain breaks: 1 Chain: "D" Number of atoms: 2780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2780 Classifications: {'peptide': 343} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 328} Chain breaks: 1 Chain: "E" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2740 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain breaks: 1 Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 941 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 7 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 6 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 47 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'ABU': 1, 'DZP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'DZP': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'ABU': 1, 'DZP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.55, per 1000 atoms: 0.56 Number of scatterers: 15265 At special positions: 0 Unit cell: (99.345, 122.615, 135.145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 3 17.00 S 83 16.00 P 6 15.00 O 2818 8.00 N 2477 7.00 C 9878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 139 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS B 136 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 165 " distance=2.05 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.02 Simple disulfide: pdb=" SG CYS E 136 " - pdb=" SG CYS E 150 " distance=2.03 Simple disulfide: pdb=" SG CYS G 428 " - pdb=" SG CYS G 501 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 7 " " MAN F 4 " - " MAN F 5 " " BMA I 3 " - " MAN I 6 " " MAN I 4 " - " MAN I 5 " " BMA K 3 " - " MAN K 4 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 6 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 5 " " BMA M 3 " - " MAN M 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG F 1 " - " ASN A 111 " " NAG H 1 " - " ASN B 80 " " NAG I 1 " - " ASN B 149 " " NAG J 1 " - " ASN C 208 " " NAG K 1 " - " ASN D 111 " " NAG L 1 " - " ASN E 80 " " NAG M 1 " - " ASN E 149 " Time building additional restraints: 6.47 Conformation dependent library (CDL) restraints added in 2.7 seconds 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3422 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 20 sheets defined 31.9% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'A' and resid 14 through 24 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 88 through 92 Processing helix chain 'A' and resid 175 through 178 No H-bonds generated for 'chain 'A' and resid 175 through 178' Processing helix chain 'A' and resid 224 through 246 removed outlier: 4.736A pdb=" N LEU A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Proline residue: A 233 - end of helix removed outlier: 5.339A pdb=" N PHE A 245 " --> pdb=" O SER A 241 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TRP A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 274 Processing helix chain 'A' and resid 285 through 310 removed outlier: 3.548A pdb=" N LEU A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 414 removed outlier: 4.306A pdb=" N ILE A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Proline residue: A 401 - end of helix Processing helix chain 'B' and resid 10 through 20 Processing helix chain 'B' and resid 70 through 72 No H-bonds generated for 'chain 'B' and resid 70 through 72' Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 226 through 240 removed outlier: 3.852A pdb=" N TRP B 237 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL B 238 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE B 240 " --> pdb=" O SER B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 270 removed outlier: 4.044A pdb=" N ALA B 252 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 308 removed outlier: 3.865A pdb=" N TYR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 445 Proline residue: B 432 - end of helix Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 241 through 256 removed outlier: 4.337A pdb=" N SER C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE C 255 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N TRP C 256 " --> pdb=" O TRP C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 285 removed outlier: 3.848A pdb=" N THR C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE C 282 " --> pdb=" O THR C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 321 Processing helix chain 'C' and resid 407 through 434 removed outlier: 5.133A pdb=" N ASP C 411 " --> pdb=" O ALA C 408 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TYR C 413 " --> pdb=" O MET C 410 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG C 415 " --> pdb=" O SER C 412 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE C 418 " --> pdb=" O ARG C 415 " (cutoff:3.500A) Proline residue: C 419 - end of helix removed outlier: 3.539A pdb=" N PHE C 422 " --> pdb=" O PRO C 419 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR C 429 " --> pdb=" O ASN C 426 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP C 430 " --> pdb=" O LEU C 427 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 431 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 432 " --> pdb=" O TYR C 429 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR C 433 " --> pdb=" O TRP C 430 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU C 434 " --> pdb=" O VAL C 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 231 through 246 removed outlier: 4.128A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 276 removed outlier: 5.083A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 310 removed outlier: 4.069A pdb=" N PHE D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 414 Proline residue: D 401 - end of helix Processing helix chain 'E' and resid 10 through 20 Processing helix chain 'E' and resid 70 through 72 No H-bonds generated for 'chain 'E' and resid 70 through 72' Processing helix chain 'E' and resid 85 through 90 removed outlier: 3.570A pdb=" N ASP E 89 " --> pdb=" O ARG E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 142 No H-bonds generated for 'chain 'E' and resid 140 through 142' Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 226 through 241 removed outlier: 4.079A pdb=" N TRP E 237 " --> pdb=" O THR E 233 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL E 238 " --> pdb=" O ILE E 234 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N SER E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N PHE E 240 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N TRP E 241 " --> pdb=" O TRP E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 271 Processing helix chain 'E' and resid 280 through 307 removed outlier: 3.547A pdb=" N LEU E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 421 through 445 removed outlier: 4.034A pdb=" N ILE E 429 " --> pdb=" O ARG E 425 " (cutoff:3.500A) Proline residue: E 432 - end of helix Processing helix chain 'G' and resid 493 through 495 No H-bonds generated for 'chain 'G' and resid 493 through 495' Processing sheet with id= A, first strand: chain 'A' and resid 39 through 43 Processing sheet with id= B, first strand: chain 'A' and resid 118 through 121 removed outlier: 3.782A pdb=" N SER A 49 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE A 65 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL A 47 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG A 67 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ILE A 45 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.163A pdb=" N SER A 159 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 211 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 191 through 195 removed outlier: 6.754A pdb=" N HIS A 218 " --> pdb=" O LEU A 194 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 164 through 168 removed outlier: 6.337A pdb=" N VAL B 36 " --> pdb=" O GLU B 165 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TYR B 167 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 38 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N CYS B 37 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG B 68 " --> pdb=" O CYS B 37 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR B 60 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE B 47 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR B 58 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 127 " --> pdb=" O MET B 115 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 116 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 98 removed outlier: 3.507A pdb=" N GLN B 148 " --> pdb=" O LEU B 214 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS B 150 " --> pdb=" O PHE B 212 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER B 156 " --> pdb=" O PRO B 206 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER B 211 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 179 through 183 removed outlier: 5.711A pdb=" N THR C 51 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLN C 182 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ILE C 53 " --> pdb=" O GLN C 182 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU C 52 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N TYR C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP C 75 " --> pdb=" O ASN C 60 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE C 62 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR C 73 " --> pdb=" O ILE C 62 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ARG C 138 " --> pdb=" O TRP C 134 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR C 142 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU C 131 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 57 through 59 Processing sheet with id= I, first strand: chain 'C' and resid 111 through 113 removed outlier: 4.798A pdb=" N SER C 171 " --> pdb=" O VAL C 221 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL C 221 " --> pdb=" O SER C 171 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER C 230 " --> pdb=" O PHE C 203 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N PHE C 203 " --> pdb=" O SER C 230 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 116 through 121 removed outlier: 6.581A pdb=" N ASP C 148 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA C 119 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR C 146 " --> pdb=" O ALA C 119 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.066A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 69 through 71 Processing sheet with id= M, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= N, first strand: chain 'D' and resid 150 through 154 Processing sheet with id= O, first strand: chain 'D' and resid 196 through 204 Processing sheet with id= P, first strand: chain 'E' and resid 164 through 168 removed outlier: 6.318A pdb=" N VAL E 36 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N TYR E 167 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL E 38 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N CYS E 37 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ARG E 68 " --> pdb=" O CYS E 37 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR E 60 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE E 47 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR E 58 " --> pdb=" O ILE E 47 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 96 through 98 Processing sheet with id= R, first strand: chain 'E' and resid 186 through 188 Processing sheet with id= S, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.723A pdb=" N GLN G 5 " --> pdb=" O ALA G 429 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 498 through 502 removed outlier: 3.576A pdb=" N MET G 440 " --> pdb=" O MET G 457 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG G 444 " --> pdb=" O PHE G 453 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE G 453 " --> pdb=" O ARG G 444 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA G 446 " --> pdb=" O ARG G 451 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ARG G 451 " --> pdb=" O ALA G 446 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1737 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: 4.49 Time building geometry restraints manager: 6.91 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: 2818 1.32 - 1.45: 4347 1.45 - 1.57: 8330 1.57 - 1.69: 10 1.69 - 1.82: 146 Bond restraints: 15651 Sorted by residual: bond pdb=" CB THR C 215 " pdb=" CG2 THR C 215 " ideal model delta sigma weight residual 1.521 1.383 0.138 3.30e-02 9.18e+02 1.74e+01 bond pdb=" O4 PIO D2002 " pdb=" P4 PIO D2002 " ideal model delta sigma weight residual 1.648 1.574 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O4 PIO A 501 " pdb=" P4 PIO A 501 " ideal model delta sigma weight residual 1.648 1.579 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1B PIO D2002 " pdb=" O3C PIO D2002 " ideal model delta sigma weight residual 1.399 1.332 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" O5 PIO A 501 " pdb=" P5 PIO A 501 " ideal model delta sigma weight residual 1.648 1.582 0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 15646 not shown) Histogram of bond angle deviations from ideal: 94.76 - 102.99: 122 102.99 - 111.22: 6541 111.22 - 119.45: 6570 119.45 - 127.68: 7878 127.68 - 135.91: 159 Bond angle restraints: 21270 Sorted by residual: angle pdb=" N ILE B 281 " pdb=" CA ILE B 281 " pdb=" C ILE B 281 " ideal model delta sigma weight residual 113.43 101.90 11.53 1.09e+00 8.42e-01 1.12e+02 angle pdb=" N VAL A 64 " pdb=" CA VAL A 64 " pdb=" C VAL A 64 " ideal model delta sigma weight residual 108.85 124.03 -15.18 1.54e+00 4.22e-01 9.72e+01 angle pdb=" N ALA G 505 " pdb=" CA ALA G 505 " pdb=" C ALA G 505 " ideal model delta sigma weight residual 108.41 94.76 13.65 1.63e+00 3.76e-01 7.01e+01 angle pdb=" N TRP G 508 " pdb=" CA TRP G 508 " pdb=" C TRP G 508 " ideal model delta sigma weight residual 111.39 100.13 11.26 1.38e+00 5.25e-01 6.66e+01 angle pdb=" N ASP B 146 " pdb=" CA ASP B 146 " pdb=" C ASP B 146 " ideal model delta sigma weight residual 110.48 119.42 -8.94 1.48e+00 4.57e-01 3.65e+01 ... (remaining 21265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.56: 9188 29.56 - 59.11: 72 59.11 - 88.67: 39 88.67 - 118.22: 28 118.22 - 147.78: 9 Dihedral angle restraints: 9336 sinusoidal: 4014 harmonic: 5322 Sorted by residual: dihedral pdb=" CB CYS E 136 " pdb=" SG CYS E 136 " pdb=" SG CYS E 150 " pdb=" CB CYS E 150 " ideal model delta sinusoidal sigma weight residual 93.00 146.85 -53.85 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CA LEU B 79 " pdb=" C LEU B 79 " pdb=" N ASN B 80 " pdb=" CA ASN B 80 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP E 30 " pdb=" C ASP E 30 " pdb=" N PHE E 31 " pdb=" CA PHE E 31 " ideal model delta harmonic sigma weight residual -180.00 -153.17 -26.83 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 9333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 2403 0.185 - 0.370: 60 0.370 - 0.555: 1 0.555 - 0.740: 1 0.740 - 0.925: 2 Chirality restraints: 2467 Sorted by residual: chirality pdb=" C1 MAN I 4 " pdb=" O6 BMA I 3 " pdb=" C2 MAN I 4 " pdb=" O5 MAN I 4 " both_signs ideal model delta sigma weight residual False 2.40 1.48 0.92 2.00e-02 2.50e+03 2.14e+03 chirality pdb=" C1 MAN I 6 " pdb=" O3 BMA I 3 " pdb=" C2 MAN I 6 " pdb=" O5 MAN I 6 " both_signs ideal model delta sigma weight residual False 2.40 1.78 0.62 2.00e-02 2.50e+03 9.58e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-02 2.50e+03 3.06e+02 ... (remaining 2464 not shown) Planarity restraints: 2589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.261 2.00e-02 2.50e+03 2.18e-01 5.96e+02 pdb=" C7 NAG I 1 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.366 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 DZP B 502 " -0.035 2.00e-02 2.50e+03 4.91e-02 5.43e+01 pdb=" C14 DZP B 502 " -0.034 2.00e-02 2.50e+03 pdb=" C5 DZP B 502 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DZP B 502 " -0.007 2.00e-02 2.50e+03 pdb=" C7 DZP B 502 " -0.032 2.00e-02 2.50e+03 pdb=" C8 DZP B 502 " -0.042 2.00e-02 2.50e+03 pdb=" C9 DZP B 502 " -0.027 2.00e-02 2.50e+03 pdb=" N2 DZP B 502 " 0.087 2.00e-02 2.50e+03 pdb="CL DZP B 502 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 DZP B 502 " -0.046 2.00e-02 2.50e+03 5.27e-02 4.16e+01 pdb=" C18 DZP B 502 " -0.022 2.00e-02 2.50e+03 pdb=" C20 DZP B 502 " -0.042 2.00e-02 2.50e+03 pdb=" C6 DZP B 502 " 0.072 2.00e-02 2.50e+03 pdb=" N2 DZP B 502 " -0.038 2.00e-02 2.50e+03 pdb=" O1 DZP B 502 " 0.075 2.00e-02 2.50e+03 ... (remaining 2586 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3552 2.78 - 3.31: 13377 3.31 - 3.84: 25940 3.84 - 4.37: 30444 4.37 - 4.90: 52426 Nonbonded interactions: 125739 Sorted by model distance: nonbonded pdb=" OH TYR E 57 " pdb=" O THR E 151 " model vdw 2.251 2.440 nonbonded pdb=" O THR B 233 " pdb=" OG SER B 236 " model vdw 2.275 2.440 nonbonded pdb=" O SER D 244 " pdb=" NH1 ARG D 255 " model vdw 2.292 2.520 nonbonded pdb=" O VAL C 248 " pdb=" OG SER C 251 " model vdw 2.295 2.440 nonbonded pdb=" O LEU B 253 " pdb=" OG1 THR B 257 " model vdw 2.301 2.440 ... (remaining 125734 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 13 through 320 or resid 384 through 418)) selection = (chain 'D' and resid 13 through 418) } ncs_group { reference = (chain 'B' and (resid 8 through 312 or resid 419 through 447 or resid 501 throug \ h 502)) selection = chain 'E' } ncs_group { reference = (chain 'F' and (resid 2 or resid 5 through 7)) selection = (chain 'I' and (resid 1 or resid 4 through 6)) selection = (chain 'M' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } 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: 0.900 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: 6.070 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 43.630 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.100 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 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 : 0.013 0.138 15651 Z= 0.872 Angle : 1.194 15.183 21270 Z= 0.656 Chirality : 0.078 0.925 2467 Planarity : 0.010 0.218 2582 Dihedral : 13.874 147.778 5896 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.35 % Cis-general : 0.29 % 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: -3.42 (0.17), residues: 1784 helix: -1.65 (0.17), residues: 561 sheet: -2.32 (0.22), residues: 459 loop : -2.59 (0.19), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP C 252 HIS 0.025 0.004 HIS A 102 PHE 0.057 0.005 PHE B 105 TYR 0.063 0.005 TYR C 181 ARG 0.025 0.002 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3568 Ramachandran restraints generated. 1784 Oldfield, 0 Emsley, 1784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 527 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.8876 (mttt) cc_final: 0.8578 (mtpp) REVERT: A 106 LYS cc_start: 0.8280 (tptt) cc_final: 0.8058 (tptp) REVERT: A 294 TYR cc_start: 0.8590 (t80) cc_final: 0.8064 (t80) REVERT: B 112 LYS cc_start: 0.8774 (tttt) cc_final: 0.8377 (ttmm) REVERT: B 155 GLU cc_start: 0.8119 (tt0) cc_final: 0.7842 (tt0) REVERT: B 173 LYS cc_start: 0.8995 (mttt) cc_final: 0.8794 (mtmm) REVERT: B 227 MET cc_start: 0.7909 (mmm) cc_final: 0.7414 (mmt) REVERT: B 267 HIS cc_start: 0.7946 (m90) cc_final: 0.7508 (m90) REVERT: B 274 LYS cc_start: 0.8892 (mttt) cc_final: 0.8681 (mttt) REVERT: B 283 MET cc_start: 0.8835 (mmm) cc_final: 0.8377 (mmm) REVERT: B 286 MET cc_start: 0.7779 (mtp) cc_final: 0.7512 (mtp) REVERT: B 301 PHE cc_start: 0.8888 (t80) cc_final: 0.8595 (t80) REVERT: B 426 TRP cc_start: 0.8697 (t60) cc_final: 0.7667 (t60) REVERT: C 71 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7681 (mt-10) REVERT: C 136 ASP cc_start: 0.9037 (p0) cc_final: 0.8599 (p0) REVERT: C 162 GLU cc_start: 0.7623 (pt0) cc_final: 0.7222 (mt-10) REVERT: C 219 ASP cc_start: 0.7446 (m-30) cc_final: 0.7198 (m-30) REVERT: C 241 TYR cc_start: 0.7091 (m-10) cc_final: 0.6817 (m-80) REVERT: D 148 MET cc_start: 0.7977 (mpp) cc_final: 0.7418 (mpp) REVERT: D 156 LYS cc_start: 0.9017 (mttt) cc_final: 0.8798 (mtpp) REVERT: D 192 ASP cc_start: 0.8437 (m-30) cc_final: 0.8230 (m-30) REVERT: D 213 MET cc_start: 0.8679 (mmp) cc_final: 0.8012 (mmt) REVERT: E 24 ASP cc_start: 0.8114 (t0) cc_final: 0.7883 (t0) REVERT: E 112 LYS cc_start: 0.9004 (tttt) cc_final: 0.8759 (tttp) REVERT: E 227 MET cc_start: 0.7361 (mmm) cc_final: 0.6893 (tmm) REVERT: G 424 LEU cc_start: 0.8362 (tp) cc_final: 0.7981 (tp) REVERT: G 438 TYR cc_start: 0.8858 (m-80) cc_final: 0.8378 (m-80) REVERT: G 478 ASP cc_start: 0.8255 (t0) cc_final: 0.7673 (t0) REVERT: G 488 LEU cc_start: 0.8826 (mp) cc_final: 0.8589 (mt) REVERT: G 510 LEU cc_start: 0.8374 (mt) cc_final: 0.8169 (mt) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.3317 time to fit residues: 240.2987 Evaluate side-chains 294 residues out of total 1612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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-1.21-5211/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: 60.9128 > 50: distance: 34 - 52: 21.559 distance: 39 - 60: 23.260 distance: 43 - 69: 31.594 distance: 47 - 52: 24.709 distance: 48 - 77: 5.871 distance: 52 - 53: 28.800 distance: 53 - 54: 30.010 distance: 53 - 56: 34.021 distance: 54 - 55: 56.092 distance: 54 - 60: 50.908 distance: 56 - 57: 28.947 distance: 57 - 58: 6.073 distance: 57 - 59: 17.446 distance: 60 - 61: 32.813 distance: 61 - 62: 38.051 distance: 61 - 64: 49.927 distance: 62 - 63: 27.049 distance: 62 - 69: 31.380 distance: 64 - 65: 43.269 distance: 65 - 66: 24.130 distance: 66 - 67: 5.580 distance: 67 - 68: 15.220 distance: 69 - 70: 44.408 distance: 70 - 71: 45.109 distance: 70 - 73: 25.279 distance: 71 - 72: 34.347 distance: 71 - 77: 22.772 distance: 73 - 74: 36.619 distance: 74 - 75: 28.122 distance: 74 - 76: 24.223 distance: 77 - 78: 17.612 distance: 78 - 79: 21.664 distance: 78 - 81: 9.405 distance: 79 - 80: 23.979 distance: 79 - 85: 13.539 distance: 81 - 82: 20.097 distance: 82 - 83: 18.627 distance: 82 - 84: 18.471 distance: 85 - 86: 26.138 distance: 86 - 87: 23.564 distance: 86 - 89: 29.644 distance: 87 - 88: 30.531 distance: 87 - 94: 51.988 distance: 89 - 90: 23.584 distance: 90 - 91: 22.483 distance: 91 - 92: 34.986 distance: 92 - 93: 37.345 distance: 94 - 95: 34.158 distance: 95 - 96: 11.734 distance: 96 - 97: 38.708 distance: 96 - 98: 15.726 distance: 98 - 99: 17.000 distance: 99 - 100: 20.454 distance: 99 - 102: 26.812 distance: 100 - 101: 36.157 distance: 100 - 110: 13.400 distance: 102 - 103: 12.855 distance: 103 - 104: 11.475 distance: 103 - 105: 9.641 distance: 104 - 106: 18.814 distance: 105 - 107: 8.252 distance: 106 - 108: 3.999 distance: 107 - 108: 3.859 distance: 108 - 109: 6.210 distance: 110 - 111: 19.732 distance: 111 - 112: 5.005 distance: 111 - 114: 27.189 distance: 112 - 113: 33.048 distance: 112 - 118: 41.088 distance: 114 - 115: 17.640 distance: 115 - 116: 19.110 distance: 115 - 117: 7.784 distance: 118 - 119: 16.943 distance: 119 - 120: 36.785 distance: 119 - 122: 25.097 distance: 120 - 121: 57.904 distance: 120 - 126: 41.249 distance: 122 - 123: 13.127 distance: 122 - 124: 14.328 distance: 123 - 125: 14.282 distance: 126 - 127: 23.766 distance: 127 - 128: 11.575 distance: 127 - 130: 7.723 distance: 128 - 129: 9.095 distance: 128 - 137: 7.458 distance: 130 - 131: 14.265 distance: 132 - 133: 4.149 distance: 133 - 134: 9.951 distance: 134 - 135: 4.715 distance: 134 - 136: 11.635