Starting phenix.real_space_refine on Thu Jan 18 10:28:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbf_24978/01_2024/7sbf_24978_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbf_24978/01_2024/7sbf_24978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbf_24978/01_2024/7sbf_24978.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbf_24978/01_2024/7sbf_24978.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbf_24978/01_2024/7sbf_24978_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sbf_24978/01_2024/7sbf_24978_updated.pdb" } resolution = 2.9 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= 1.000 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 65 5.16 5 C 5452 2.51 5 N 1450 2.21 5 O 1558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 251": "OD1" <-> "OD2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B ASP 186": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 258": "OD1" <-> "OD2" Residue "B PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8525 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1683 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 2537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2537 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 381 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 48} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1742 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2182 Unusual residues: {'8QY': 1} Classifications: {'peptide': 281, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270, None: 1} Not linked: pdbres="ARG R 345 " pdbres="8QY R 501 " Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 43 Time building chain proxies: 5.10, per 1000 atoms: 0.60 Number of scatterers: 8525 At special positions: 0 Unit cell: (98.58, 116.6, 115.54, 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 65 16.00 O 1558 8.00 N 1450 7.00 C 5452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS R 140 " - pdb=" SG CYS R 217 " distance=2.04 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: 3.50 Conformation dependent library (CDL) restraints added in 1.8 seconds 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 14 sheets defined 34.4% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 46 through 52 removed outlier: 4.048A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 52' Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 274 through 280 removed outlier: 3.685A pdb=" N ILE A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 274 through 280' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.340A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 6 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.216A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'C' and resid 10 through 23 removed outlier: 3.610A pdb=" N LYS C 14 " --> pdb=" O ALA C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'R' and resid 66 through 96 removed outlier: 4.232A pdb=" N THR R 72 " --> pdb=" O ALA R 68 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 130 removed outlier: 3.906A pdb=" N THR R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) Proline residue: R 122 - end of helix Processing helix chain 'R' and resid 136 through 139 No H-bonds generated for 'chain 'R' and resid 136 through 139' Processing helix chain 'R' and resid 143 through 170 removed outlier: 3.617A pdb=" N PHE R 152 " --> pdb=" O TYR R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 178 removed outlier: 3.666A pdb=" N ASP R 177 " --> pdb=" O VAL R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 205 removed outlier: 3.714A pdb=" N ALA R 197 " --> pdb=" O ILE R 193 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE R 198 " --> pdb=" O LEU R 194 " (cutoff:3.500A) Proline residue: R 201 - end of helix Processing helix chain 'R' and resid 225 through 240 removed outlier: 4.748A pdb=" N ASN R 230 " --> pdb=" O TRP R 226 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 261 removed outlier: 3.870A pdb=" N VAL R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER R 261 " --> pdb=" O LEU R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 263 through 265 No H-bonds generated for 'chain 'R' and resid 263 through 265' Processing helix chain 'R' and resid 269 through 305 Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 312 through 336 removed outlier: 3.877A pdb=" N VAL R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER R 329 " --> pdb=" O GLY R 325 " (cutoff:3.500A) Proline residue: R 333 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.512A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.856A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.940A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.836A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 203 removed outlier: 4.139A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.689A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.544A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.614A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 Processing sheet with id= K, first strand: chain 'E' and resid 92 through 99 removed outlier: 6.021A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 134 through 136 removed outlier: 6.484A pdb=" N LYS E 232 " --> pdb=" O VAL E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 143 through 148 Processing sheet with id= N, first strand: chain 'E' and resid 213 through 219 removed outlier: 5.868A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1128 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: 2.47 Time building geometry restraints manager: 3.79 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: 2710 1.34 - 1.46: 1866 1.46 - 1.58: 4032 1.58 - 1.69: 3 1.69 - 1.81: 94 Bond restraints: 8705 Sorted by residual: bond pdb=" C02 8QY R 501 " pdb=" N03 8QY R 501 " ideal model delta sigma weight residual 1.365 1.441 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" C02 8QY R 501 " pdb=" N12 8QY R 501 " ideal model delta sigma weight residual 1.360 1.423 -0.063 2.00e-02 2.50e+03 9.98e+00 bond pdb=" N ILE R 142 " pdb=" CA ILE R 142 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.82e+00 bond pdb=" C04 8QY R 501 " pdb=" N03 8QY R 501 " ideal model delta sigma weight residual 1.449 1.500 -0.051 2.00e-02 2.50e+03 6.38e+00 bond pdb=" C13 8QY R 501 " pdb=" C14 8QY R 501 " ideal model delta sigma weight residual 1.536 1.586 -0.050 2.00e-02 2.50e+03 6.30e+00 ... (remaining 8700 not shown) Histogram of bond angle deviations from ideal: 91.28 - 99.82: 5 99.82 - 108.37: 363 108.37 - 116.92: 5747 116.92 - 125.47: 5573 125.47 - 134.02: 138 Bond angle restraints: 11826 Sorted by residual: angle pdb=" N LYS R 141 " pdb=" CA LYS R 141 " pdb=" C LYS R 141 " ideal model delta sigma weight residual 113.17 103.06 10.11 1.26e+00 6.30e-01 6.43e+01 angle pdb=" C ILE B 18 " pdb=" N ARG B 19 " pdb=" CA ARG B 19 " ideal model delta sigma weight residual 121.14 114.16 6.98 1.75e+00 3.27e-01 1.59e+01 angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 113.16 108.30 4.86 1.24e+00 6.50e-01 1.54e+01 angle pdb=" C ARG B 19 " pdb=" N ASP B 20 " pdb=" CA ASP B 20 " ideal model delta sigma weight residual 121.58 114.47 7.11 1.95e+00 2.63e-01 1.33e+01 angle pdb=" CA ILE R 142 " pdb=" C ILE R 142 " pdb=" O ILE R 142 " ideal model delta sigma weight residual 120.78 116.33 4.45 1.25e+00 6.40e-01 1.27e+01 ... (remaining 11821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 4715 17.74 - 35.48: 366 35.48 - 53.23: 36 53.23 - 70.97: 10 70.97 - 88.71: 7 Dihedral angle restraints: 5134 sinusoidal: 1883 harmonic: 3251 Sorted by residual: dihedral pdb=" CB CYS R 140 " pdb=" SG CYS R 140 " pdb=" SG CYS R 217 " pdb=" CB CYS R 217 " ideal model delta sinusoidal sigma weight residual -86.00 -162.14 76.14 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CA TYR E 101 " pdb=" C TYR E 101 " pdb=" N TYR E 102 " pdb=" CA TYR E 102 " ideal model delta harmonic sigma weight residual 180.00 160.90 19.10 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER R 268 " pdb=" C SER R 268 " pdb=" N LYS R 269 " pdb=" CA LYS R 269 " ideal model delta harmonic sigma weight residual 180.00 -160.95 -19.05 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 5131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1171 0.065 - 0.131: 192 0.131 - 0.196: 6 0.196 - 0.261: 0 0.261 - 0.327: 3 Chirality restraints: 1372 Sorted by residual: chirality pdb=" C14 8QY R 501 " pdb=" C13 8QY R 501 " pdb=" C15 8QY R 501 " pdb=" N23 8QY R 501 " both_signs ideal model delta sigma weight residual False 2.36 2.69 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ASP B 247 " pdb=" N ASP B 247 " pdb=" C ASP B 247 " pdb=" CB ASP B 247 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA LYS R 141 " pdb=" N LYS R 141 " pdb=" C LYS R 141 " pdb=" CB LYS R 141 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 1369 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 308 " -0.039 5.00e-02 4.00e+02 5.81e-02 5.39e+00 pdb=" N PRO R 309 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO R 309 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 309 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO B 236 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 83 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C LEU R 83 " 0.033 2.00e-02 2.50e+03 pdb=" O LEU R 83 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE R 84 " -0.011 2.00e-02 2.50e+03 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 734 2.74 - 3.28: 8523 3.28 - 3.82: 14266 3.82 - 4.36: 17181 4.36 - 4.90: 30137 Nonbonded interactions: 70841 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.200 2.440 nonbonded pdb=" OG SER E 149 " pdb=" O LYS E 151 " model vdw 2.244 2.440 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.265 2.520 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.268 2.440 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.299 2.520 ... (remaining 70836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.490 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: 2.620 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.580 Find NCS groups from input model: 0.240 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.005 0.082 8705 Z= 0.305 Angle : 0.652 10.106 11826 Z= 0.357 Chirality : 0.047 0.327 1372 Planarity : 0.004 0.058 1485 Dihedral : 12.821 88.712 3027 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer: Outliers : 0.23 % Allowed : 0.68 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1103 helix: 0.92 (0.28), residues: 367 sheet: -0.37 (0.28), residues: 289 loop : -0.41 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE A 274 TYR 0.017 0.002 TYR A 296 ARG 0.003 0.000 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 1.031 Fit side-chains REVERT: A 245 GLU cc_start: 0.7139 (mp0) cc_final: 0.6905 (mp0) REVERT: A 247 MET cc_start: 0.8579 (mtp) cc_final: 0.8330 (mtp) REVERT: A 273 LEU cc_start: 0.8744 (tp) cc_final: 0.8522 (tm) REVERT: A 308 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 337 ASP cc_start: 0.7884 (m-30) cc_final: 0.7655 (m-30) REVERT: R 86 ASN cc_start: 0.7868 (m-40) cc_final: 0.7653 (m-40) REVERT: R 87 PHE cc_start: 0.8036 (m-10) cc_final: 0.7423 (m-80) REVERT: R 190 CYS cc_start: 0.8128 (t) cc_final: 0.7834 (t) REVERT: R 342 ASN cc_start: 0.7970 (m-40) cc_final: 0.7714 (m-40) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 1.1884 time to fit residues: 241.2961 Evaluate side-chains 143 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 0.2980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 256 ASN B 268 ASN C 59 ASN E 167 GLN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8705 Z= 0.193 Angle : 0.540 8.940 11826 Z= 0.280 Chirality : 0.042 0.133 1372 Planarity : 0.003 0.042 1485 Dihedral : 6.223 89.514 1221 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.94 % Allowed : 13.25 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1103 helix: 1.40 (0.28), residues: 351 sheet: -0.36 (0.29), residues: 280 loop : -0.29 (0.31), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE R 135 TYR 0.017 0.001 TYR A 296 ARG 0.002 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.006 Fit side-chains REVERT: A 14 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: A 247 MET cc_start: 0.8480 (mtp) cc_final: 0.8246 (mtp) REVERT: A 337 ASP cc_start: 0.7837 (m-30) cc_final: 0.7546 (m-30) REVERT: B 19 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7249 (ptt-90) REVERT: R 87 PHE cc_start: 0.8077 (m-10) cc_final: 0.7626 (m-80) REVERT: R 130 MET cc_start: 0.8095 (mpp) cc_final: 0.7819 (mpp) REVERT: R 258 ARG cc_start: 0.7914 (tmt170) cc_final: 0.7675 (tmt170) outliers start: 26 outliers final: 13 residues processed: 168 average time/residue: 1.2301 time to fit residues: 219.9209 Evaluate side-chains 161 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 ASN A 256 ASN A 306 GLN B 13 GLN B 268 ASN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8705 Z= 0.276 Angle : 0.562 9.323 11826 Z= 0.292 Chirality : 0.043 0.135 1372 Planarity : 0.003 0.044 1485 Dihedral : 6.054 86.391 1221 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.72 % Favored : 96.19 % Rotamer: Outliers : 4.30 % Allowed : 17.33 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1103 helix: 1.44 (0.28), residues: 353 sheet: -0.34 (0.29), residues: 281 loop : -0.36 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.003 0.001 HIS R 297 PHE 0.012 0.001 PHE A 189 TYR 0.012 0.002 TYR E 178 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 152 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7809 (tt0) REVERT: A 20 ASP cc_start: 0.7800 (t0) cc_final: 0.7444 (m-30) REVERT: A 273 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8353 (mm) REVERT: A 337 ASP cc_start: 0.7861 (m-30) cc_final: 0.7552 (m-30) REVERT: B 19 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7124 (ptt-90) REVERT: B 156 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: R 65 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7220 (tt) REVERT: R 87 PHE cc_start: 0.8149 (m-10) cc_final: 0.7660 (m-80) REVERT: R 130 MET cc_start: 0.8088 (mpp) cc_final: 0.7748 (mpp) REVERT: R 258 ARG cc_start: 0.7925 (tmt170) cc_final: 0.7645 (tmt170) outliers start: 38 outliers final: 21 residues processed: 173 average time/residue: 1.1692 time to fit residues: 215.6002 Evaluate side-chains 169 residues out of total 965 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 143 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 174 GLN Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 195 SER Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 236 VAL Chi-restraints excluded: chain R residue 261 SER Chi-restraints excluded: chain R residue 330 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 50.3393 > 50: distance: 56 - 131: 34.148 distance: 70 - 120: 4.488 distance: 73 - 117: 8.688 distance: 101 - 102: 3.531 distance: 102 - 103: 6.893 distance: 102 - 105: 3.596 distance: 103 - 104: 8.103 distance: 105 - 106: 5.974 distance: 106 - 107: 4.711 distance: 107 - 108: 5.663 distance: 108 - 109: 4.242 distance: 109 - 110: 3.431 distance: 112 - 113: 6.117 distance: 113 - 116: 4.997 distance: 114 - 115: 3.695 distance: 114 - 117: 4.213 distance: 117 - 118: 4.424 distance: 119 - 121: 3.427 distance: 122 - 123: 3.082 distance: 122 - 125: 5.504 distance: 123 - 124: 4.729 distance: 123 - 128: 8.325 distance: 125 - 126: 6.307 distance: 125 - 127: 8.750 distance: 128 - 129: 3.564 distance: 129 - 130: 9.638 distance: 129 - 132: 7.068 distance: 130 - 131: 31.959 distance: 130 - 136: 16.976 distance: 132 - 133: 5.056 distance: 133 - 134: 12.292 distance: 133 - 135: 17.024 distance: 136 - 137: 27.994 distance: 137 - 138: 18.749 distance: 137 - 140: 31.429 distance: 138 - 139: 20.974 distance: 138 - 141: 19.786 distance: 141 - 142: 13.806 distance: 142 - 143: 8.275 distance: 143 - 144: 10.472 distance: 143 - 145: 6.428 distance: 145 - 146: 4.217 distance: 146 - 147: 5.826 distance: 146 - 149: 4.350 distance: 147 - 148: 9.336 distance: 147 - 155: 7.155 distance: 149 - 150: 5.907 distance: 150 - 152: 5.552 distance: 152 - 154: 14.027 distance: 153 - 154: 9.493 distance: 156 - 157: 4.267 distance: 156 - 159: 6.779 distance: 157 - 158: 11.288 distance: 160 - 161: 15.185 distance: 161 - 162: 13.581 distance: 161 - 164: 20.621 distance: 162 - 163: 3.398 distance: 164 - 165: 7.001 distance: 165 - 166: 8.919 distance: 165 - 167: 5.229