Starting phenix.real_space_refine on Tue Jul 29 02:22:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tzf_26208/07_2025/7tzf_26208.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tzf_26208/07_2025/7tzf_26208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tzf_26208/07_2025/7tzf_26208.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tzf_26208/07_2025/7tzf_26208.map" model { file = "/net/cci-nas-00/data/ceres_data/7tzf_26208/07_2025/7tzf_26208.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tzf_26208/07_2025/7tzf_26208.cif" } resolution = 2.4 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 72 5.16 5 C 6640 2.51 5 N 1733 2.21 5 O 1896 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10342 Number of models: 1 Model: "" Number of chains: 14 Chain: "E" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 755 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 7, 'TRANS': 106} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 199 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 90 Chain: "P" Number of atoms: 284 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Conformer: "C" Number of residues, atoms: 37, 273 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} bond proxies already assigned to first conformer: 265 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 3006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 3006 Classifications: {'peptide': 367} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 16, 'TRANS': 350} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1898 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2600 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'P42': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 310 Unusual residues: {'NAG': 3, 'PLM': 11, 'Y01': 2} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG P 18 " occ=0.50 ... (20 atoms not shown) pdb=" NH2CARG P 18 " occ=0.62 Time building chain proxies: 7.42, per 1000 atoms: 0.72 Number of scatterers: 10342 At special positions: 0 Unit cell: (84.5, 99.45, 163.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 1 15.00 O 1896 8.00 N 1733 7.00 C 6640 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Links applied NAG-ASN " NAG E 201 " - " ASN E 71 " " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " " NAG R 503 " - " ASN R 125 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.5 seconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 13 sheets defined 44.7% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'E' and resid 30 through 37 removed outlier: 4.046A pdb=" N LEU E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.803A pdb=" N LYS E 42 " --> pdb=" O PRO E 38 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA E 43 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 81 removed outlier: 3.809A pdb=" N GLU E 67 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS E 72 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 77 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 101 removed outlier: 3.624A pdb=" N GLN E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 141 Proline residue: E 121 - end of helix Proline residue: E 126 - end of helix Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'R' and resid 42 through 62 removed outlier: 4.041A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLN R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 136 removed outlier: 4.315A pdb=" N ASN R 135 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 173 removed outlier: 3.771A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 177 Processing helix chain 'R' and resid 178 through 205 Processing helix chain 'R' and resid 208 through 215 removed outlier: 3.530A pdb=" N VAL R 212 " --> pdb=" O ASN R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 249 removed outlier: 3.883A pdb=" N LYS R 220 " --> pdb=" O PRO R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 267 Processing helix chain 'R' and resid 270 through 284 removed outlier: 3.529A pdb=" N THR R 274 " --> pdb=" O PRO R 270 " (cutoff:3.500A) Processing helix chain 'R' and resid 287 through 291 Processing helix chain 'R' and resid 295 through 297 No H-bonds generated for 'chain 'R' and resid 295 through 297' Processing helix chain 'R' and resid 298 through 330 Proline residue: R 304 - end of helix removed outlier: 3.619A pdb=" N THR R 330 " --> pdb=" O LYS R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 333 through 353 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 359 Processing helix chain 'R' and resid 365 through 382 Processing helix chain 'R' and resid 382 through 392 Processing helix chain 'R' and resid 395 through 407 Processing helix chain 'A' and resid 12 through 40 removed outlier: 4.078A pdb=" N GLU A 16 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 17 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 removed outlier: 3.814A pdb=" N MET A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 239 removed outlier: 3.536A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.535A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.320A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.558A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 391 removed outlier: 4.404A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.559A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.505A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 71 through 72 Processing sheet with id=AA2, first strand: chain 'R' and resid 75 through 76 Processing sheet with id=AA3, first strand: chain 'R' and resid 90 through 94 removed outlier: 3.734A pdb=" N LYS R 110 " --> pdb=" O SER R 91 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.346A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.580A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.554A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.692A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.547A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.576A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.053A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.716A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB4, first strand: chain 'N' and resid 11 through 12 removed outlier: 6.829A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 503 hydrogen bonds defined for protein. 1441 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.15 Time building geometry restraints manager: 3.21 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: 1664 1.32 - 1.44: 2888 1.44 - 1.57: 5888 1.57 - 1.69: 2 1.69 - 1.81: 102 Bond restraints: 10544 Sorted by residual: bond pdb=" N VAL P 32 " pdb=" CA VAL P 32 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.25e-02 6.40e+03 1.09e+01 bond pdb=" OBN P42 P 101 " pdb=" PBM P42 P 101 " ideal model delta sigma weight residual 1.657 1.605 0.052 2.00e-02 2.50e+03 6.69e+00 bond pdb=" N THR P 36 " pdb=" CA THR P 36 " ideal model delta sigma weight residual 1.453 1.486 -0.033 1.27e-02 6.20e+03 6.67e+00 bond pdb=" CA SER P 34 " pdb=" CB SER P 34 " ideal model delta sigma weight residual 1.528 1.493 0.036 1.56e-02 4.11e+03 5.21e+00 bond pdb=" C4 P42 P 101 " pdb=" OBN P42 P 101 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.18e+00 ... (remaining 10539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 13896 1.46 - 2.91: 316 2.91 - 4.37: 31 4.37 - 5.83: 10 5.83 - 7.28: 2 Bond angle restraints: 14255 Sorted by residual: angle pdb=" CA GLY P 33 " pdb=" C GLY P 33 " pdb=" O GLY P 33 " ideal model delta sigma weight residual 121.92 118.21 3.71 1.05e+00 9.07e-01 1.25e+01 angle pdb=" CA THR P 36 " pdb=" C THR P 36 " pdb=" O THR P 36 " ideal model delta sigma weight residual 121.88 118.40 3.48 1.13e+00 7.83e-01 9.50e+00 angle pdb=" CA SER P 34 " pdb=" C SER P 34 " pdb=" O SER P 34 " ideal model delta sigma weight residual 120.55 117.75 2.80 1.06e+00 8.90e-01 6.99e+00 angle pdb=" C LEU E 119 " pdb=" N ILE E 120 " pdb=" CA ILE E 120 " ideal model delta sigma weight residual 120.33 122.29 -1.96 8.00e-01 1.56e+00 6.02e+00 angle pdb=" CA VAL P 32 " pdb=" C VAL P 32 " pdb=" O VAL P 32 " ideal model delta sigma weight residual 120.78 118.05 2.73 1.25e+00 6.40e-01 4.78e+00 ... (remaining 14250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.81: 6133 25.81 - 51.62: 272 51.62 - 77.42: 41 77.42 - 103.23: 9 103.23 - 129.04: 3 Dihedral angle restraints: 6458 sinusoidal: 2746 harmonic: 3712 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 172.70 -79.70 1 1.00e+01 1.00e-02 7.88e+01 dihedral pdb=" CB CYS E 40 " pdb=" SG CYS E 40 " pdb=" SG CYS E 72 " pdb=" CB CYS E 72 " ideal model delta sinusoidal sigma weight residual 93.00 169.23 -76.23 1 1.00e+01 1.00e-02 7.32e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -32.98 -53.02 1 1.00e+01 1.00e-02 3.83e+01 ... (remaining 6455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1276 0.050 - 0.100: 246 0.100 - 0.150: 54 0.150 - 0.199: 1 0.199 - 0.249: 1 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CA TYR P 37 " pdb=" N TYR P 37 " pdb=" C TYR P 37 " pdb=" CB TYR P 37 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CBE P42 P 101 " pdb=" CAB P42 P 101 " pdb=" CBK P42 P 101 " pdb=" OBD P42 P 101 " both_signs ideal model delta sigma weight residual False -2.32 -2.52 0.19 2.00e-01 2.50e+01 9.45e-01 chirality pdb=" CBF Y01 R 507 " pdb=" CAS Y01 R 507 " pdb=" CBD Y01 R 507 " pdb=" CBH Y01 R 507 " both_signs ideal model delta sigma weight residual False -2.45 -2.59 0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 1575 not shown) Planarity restraints: 1790 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN P 31 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C ASN P 31 " -0.037 2.00e-02 2.50e+03 pdb=" O ASN P 31 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL P 32 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN P 35 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.75e+00 pdb=" C ASN P 35 " -0.023 2.00e-02 2.50e+03 pdb=" O ASN P 35 " 0.008 2.00e-02 2.50e+03 pdb=" N THR P 36 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 236 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 ... (remaining 1787 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2322 2.78 - 3.31: 9517 3.31 - 3.84: 17592 3.84 - 4.37: 21836 4.37 - 4.90: 35982 Nonbonded interactions: 87249 Sorted by model distance: nonbonded pdb=" O LEU P 16 " pdb=" OG SER P 20 " model vdw 2.252 3.040 nonbonded pdb=" O TYR R 374 " pdb=" OG SER R 378 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.263 3.040 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.284 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O VAL B 187 " model vdw 2.285 3.040 ... (remaining 87244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 3.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.210 Find NCS groups from input model: 0.140 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:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 10558 Z= 0.213 Angle : 0.536 7.284 14285 Z= 0.297 Chirality : 0.041 0.249 1578 Planarity : 0.003 0.032 1786 Dihedral : 14.486 129.040 4035 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 1.43 % Allowed : 11.76 % Favored : 86.81 % 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: -2.36 (0.21), residues: 1257 helix: -2.10 (0.18), residues: 493 sheet: -0.34 (0.32), residues: 237 loop : -1.42 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.004 0.001 HIS R 302 PHE 0.011 0.001 PHE B 151 TYR 0.010 0.001 TYR R 391 ARG 0.004 0.000 ARG N 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 4) link_NAG-ASN : angle 2.83866 ( 12) hydrogen bonds : bond 0.23125 ( 503) hydrogen bonds : angle 8.24202 ( 1441) SS BOND : bond 0.00232 ( 9) SS BOND : angle 0.89289 ( 18) covalent geometry : bond 0.00367 (10544) covalent geometry : angle 0.52934 (14255) Misc. bond : bond 0.10561 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 177 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: P 11 ARG cc_start: 0.8475 (mtm-85) cc_final: 0.8186 (mtm-85) REVERT: P 15 PHE cc_start: 0.8283 (t80) cc_final: 0.8066 (t80) REVERT: R 99 PHE cc_start: 0.5097 (m-80) cc_final: 0.4885 (m-10) REVERT: R 141 LYS cc_start: 0.6809 (tttt) cc_final: 0.6605 (mtmt) REVERT: R 338 TYR cc_start: 0.5831 (m-80) cc_final: 0.5349 (m-10) REVERT: A 209 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: A 296 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7280 (mp) REVERT: B 46 ARG cc_start: 0.6580 (mtp85) cc_final: 0.6202 (mmm-85) REVERT: B 96 ARG cc_start: 0.7217 (mtp-110) cc_final: 0.6985 (ttp-170) REVERT: B 134 ARG cc_start: 0.6994 (ptt90) cc_final: 0.6791 (ptt90) REVERT: B 197 ARG cc_start: 0.7020 (mmm-85) cc_final: 0.6788 (mmt90) REVERT: B 268 ASN cc_start: 0.7287 (p0) cc_final: 0.7058 (p0) REVERT: G 16 VAL cc_start: 0.7614 (t) cc_final: 0.7342 (m) REVERT: N 1 GLN cc_start: 0.7578 (tp-100) cc_final: 0.7363 (tp40) REVERT: N 33 LYS cc_start: 0.8575 (ttmt) cc_final: 0.8371 (ttpt) outliers start: 15 outliers final: 5 residues processed: 189 average time/residue: 1.4893 time to fit residues: 298.6388 Evaluate side-chains 151 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 111 optimal weight: 20.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 HIS ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN P 31 ASN P 35 ASN R 52 GLN R 93 GLN R 184 HIS ** R 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 288 ASN R 336 HIS R 399 GLN A 35 GLN A 59 GLN A 254 ASN A 357 HIS B 6 GLN B 35 ASN B 75 GLN B 176 GLN B 340 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.178997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140387 restraints weight = 21918.773| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 4.89 r_work: 0.3087 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10558 Z= 0.135 Angle : 0.564 8.591 14285 Z= 0.298 Chirality : 0.042 0.139 1578 Planarity : 0.004 0.038 1786 Dihedral : 8.997 127.837 1825 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.01 % Allowed : 15.01 % Favored : 82.98 % 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: -0.46 (0.22), residues: 1257 helix: 0.35 (0.22), residues: 495 sheet: 0.10 (0.33), residues: 223 loop : -1.03 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.004 0.001 HIS A 41 PHE 0.016 0.002 PHE E 69 TYR 0.012 0.001 TYR R 131 ARG 0.007 0.001 ARG B 214 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 4) link_NAG-ASN : angle 2.94176 ( 12) hydrogen bonds : bond 0.04736 ( 503) hydrogen bonds : angle 5.04792 ( 1441) SS BOND : bond 0.00220 ( 9) SS BOND : angle 0.61554 ( 18) covalent geometry : bond 0.00281 (10544) covalent geometry : angle 0.55774 (14255) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: P 10 GLN cc_start: 0.7870 (mp-120) cc_final: 0.7498 (mm-40) REVERT: P 11 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8228 (mtm-85) REVERT: R 271 LEU cc_start: 0.7491 (mt) cc_final: 0.7140 (mt) REVERT: R 366 LYS cc_start: 0.6416 (mptt) cc_final: 0.6138 (mmtt) REVERT: A 21 GLU cc_start: 0.6153 (OUTLIER) cc_final: 0.5919 (tm-30) REVERT: A 209 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7298 (mp0) REVERT: B 13 GLN cc_start: 0.7230 (mm-40) cc_final: 0.6803 (tm-30) REVERT: B 46 ARG cc_start: 0.7367 (mtp85) cc_final: 0.6631 (mmm-85) REVERT: B 134 ARG cc_start: 0.7388 (ptt90) cc_final: 0.7148 (ptt90) REVERT: B 137 ARG cc_start: 0.8236 (tpp-160) cc_final: 0.7832 (tpt170) REVERT: N 33 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8725 (ttmt) REVERT: N 114 THR cc_start: 0.7973 (p) cc_final: 0.7698 (p) outliers start: 21 outliers final: 6 residues processed: 168 average time/residue: 1.7824 time to fit residues: 317.7169 Evaluate side-chains 153 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 212 VAL Chi-restraints excluded: chain A residue 21 GLU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.0018 > 50: distance: 57 - 82: 3.032 distance: 61 - 90: 23.845 distance: 67 - 95: 33.790 distance: 77 - 82: 5.094 distance: 78 - 101: 18.799 distance: 82 - 83: 6.305 distance: 83 - 84: 14.611 distance: 83 - 86: 8.460 distance: 84 - 85: 16.520 distance: 84 - 90: 16.226 distance: 85 - 109: 14.140 distance: 86 - 87: 11.607 distance: 88 - 89: 3.779 distance: 90 - 91: 10.849 distance: 91 - 92: 25.555 distance: 91 - 94: 7.801 distance: 92 - 93: 31.846 distance: 92 - 95: 15.371 distance: 93 - 121: 13.197 distance: 95 - 96: 47.986 distance: 96 - 97: 6.281 distance: 96 - 99: 23.560 distance: 97 - 98: 9.933 distance: 97 - 101: 28.241 distance: 98 - 132: 25.344 distance: 99 - 100: 16.348 distance: 101 - 102: 14.899 distance: 102 - 103: 9.097 distance: 102 - 105: 8.865 distance: 103 - 109: 6.246 distance: 104 - 146: 4.944 distance: 105 - 106: 8.146 distance: 106 - 108: 5.996 distance: 109 - 110: 3.091 distance: 110 - 111: 7.363 distance: 110 - 113: 3.702 distance: 111 - 112: 3.304 distance: 111 - 121: 5.165 distance: 112 - 154: 7.507 distance: 113 - 114: 5.156 distance: 114 - 115: 6.319 distance: 114 - 116: 5.066 distance: 115 - 117: 3.438 distance: 116 - 118: 4.421 distance: 117 - 119: 5.538 distance: 118 - 119: 5.241 distance: 119 - 120: 3.899 distance: 121 - 122: 5.235 distance: 122 - 125: 5.995 distance: 123 - 124: 11.407 distance: 123 - 132: 5.009 distance: 124 - 162: 26.811 distance: 125 - 126: 4.406 distance: 126 - 127: 7.085 distance: 126 - 128: 5.029 distance: 127 - 129: 5.393 distance: 128 - 130: 5.741 distance: 129 - 131: 3.579 distance: 130 - 131: 7.743 distance: 132 - 133: 8.873 distance: 133 - 134: 3.327 distance: 133 - 136: 9.746 distance: 134 - 135: 6.521 distance: 134 - 146: 6.853 distance: 135 - 168: 7.458 distance: 136 - 137: 5.204 distance: 137 - 138: 7.074 distance: 137 - 139: 10.995 distance: 138 - 140: 4.947 distance: 139 - 141: 3.154 distance: 139 - 142: 9.446 distance: 140 - 141: 9.824 distance: 141 - 143: 7.709 distance: 142 - 144: 8.171 distance: 143 - 145: 9.668 distance: 144 - 145: 3.266 distance: 146 - 147: 6.418 distance: 147 - 148: 6.296 distance: 147 - 150: 5.043 distance: 148 - 149: 3.630 distance: 148 - 154: 5.991 distance: 149 - 176: 11.659 distance: 150 - 151: 5.999 distance: 151 - 152: 24.159 distance: 152 - 153: 18.818 distance: 154 - 155: 5.749 distance: 155 - 156: 5.461 distance: 155 - 158: 8.140 distance: 156 - 157: 9.212 distance: 156 - 162: 6.023 distance: 157 - 180: 8.011 distance: 158 - 159: 6.333 distance: 159 - 160: 4.195 distance: 159 - 161: 8.192 distance: 162 - 163: 4.398 distance: 163 - 164: 5.870 distance: 163 - 166: 5.560 distance: 164 - 165: 10.086 distance: 164 - 168: 6.775 distance: 165 - 188: 11.050 distance: 166 - 167: 7.729