Starting phenix.real_space_refine on Sat Jan 20 12:57:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckw_30392/01_2024/7ckw_30392_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckw_30392/01_2024/7ckw_30392.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckw_30392/01_2024/7ckw_30392.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckw_30392/01_2024/7ckw_30392.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckw_30392/01_2024/7ckw_30392_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckw_30392/01_2024/7ckw_30392_updated.pdb" } resolution = 3.22 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7222 atoms to isotropic. 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 S 53 5.16 5 Cl 1 4.86 5 C 5158 2.51 5 N 1403 2.21 5 O 1488 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R GLU 132": "OE1" <-> "OE2" Residue "R ARG 227": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 8103 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1906 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2587 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} 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: "N" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2202 Unusual residues: {'CLR': 1, 'G3C': 1} Classifications: {'peptide': 273, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 9, 'TRANS': 263, None: 2} Not linked: pdbres="LEU R 344 " pdbres="G3C R 501 " Not linked: pdbres="G3C R 501 " pdbres="CLR R 502 " Chain breaks: 3 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 4.81, per 1000 atoms: 0.59 Number of scatterers: 8103 At special positions: 0 Unit cell: (89, 87, 123, 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) Cl 1 17.00 S 53 16.00 O 1488 8.00 N 1403 7.00 C 5158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.6 seconds 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 10 sheets defined 37.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 3.709A pdb=" N ALA A 18 " --> pdb=" O ASN A 14 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 255 through 277 removed outlier: 5.938A pdb=" N LEU A 266 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN A 271 " --> pdb=" O GLU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 294 through 301 removed outlier: 3.961A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.604A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 390 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.651A pdb=" N ILE B 33 " --> pdb=" O LEU B 30 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 44 Processing helix chain 'R' and resid 23 through 49 Processing helix chain 'R' and resid 58 through 76 removed outlier: 4.269A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 85 Processing helix chain 'R' and resid 93 through 125 removed outlier: 5.183A pdb=" N ASN R 97 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N THR R 108 " --> pdb=" O MET R 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 134 Processing helix chain 'R' and resid 137 through 160 removed outlier: 4.108A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 192 through 202 removed outlier: 3.904A pdb=" N SER R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE R 201 " --> pdb=" O SER R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 236 removed outlier: 3.849A pdb=" N ALA R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 277 removed outlier: 3.576A pdb=" N LYS R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL R 270 " --> pdb=" O ARG R 266 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 294 Proline residue: R 287 - end of helix removed outlier: 4.076A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 330 removed outlier: 4.058A pdb=" N ASP R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N VAL R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 335 through 343 removed outlier: 3.781A pdb=" N ALA R 340 " --> pdb=" O ASP R 336 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR R 343 " --> pdb=" O LYS R 339 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.004A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.747A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.744A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 208 through 212 Processing sheet with id= E, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.797A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.479A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 47 through 51 removed outlier: 7.007A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 121 through 125 removed outlier: 5.782A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 8 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 5.653A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 927 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: 2.06 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2630 1.34 - 1.46: 1961 1.46 - 1.58: 3610 1.58 - 1.69: 0 1.69 - 1.81: 73 Bond restraints: 8274 Sorted by residual: bond pdb=" C02 G3C R 501 " pdb=" O01 G3C R 501 " ideal model delta sigma weight residual 1.345 1.399 -0.054 2.00e-02 2.50e+03 7.37e+00 bond pdb=" C11 G3C R 501 " pdb=" O12 G3C R 501 " ideal model delta sigma weight residual 1.349 1.402 -0.053 2.00e-02 2.50e+03 7.03e+00 bond pdb=" N HIS A 357 " pdb=" CA HIS A 357 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 7.01e+00 bond pdb=" N PHE B 234 " pdb=" CA PHE B 234 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.30e-02 5.92e+03 6.21e+00 bond pdb=" C03 G3C R 501 " pdb=" O04 G3C R 501 " ideal model delta sigma weight residual 1.352 1.400 -0.048 2.00e-02 2.50e+03 5.72e+00 ... (remaining 8269 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.89: 188 106.89 - 113.68: 4570 113.68 - 120.48: 3246 120.48 - 127.27: 3137 127.27 - 134.06: 87 Bond angle restraints: 11228 Sorted by residual: angle pdb=" C ASP B 195 " pdb=" N THR B 196 " pdb=" CA THR B 196 " ideal model delta sigma weight residual 121.54 126.27 -4.73 1.91e+00 2.74e-01 6.14e+00 angle pdb=" N VAL R 75 " pdb=" CA VAL R 75 " pdb=" C VAL R 75 " ideal model delta sigma weight residual 113.42 111.12 2.30 1.17e+00 7.31e-01 3.86e+00 angle pdb=" CA VAL R 75 " pdb=" C VAL R 75 " pdb=" N LEU R 76 " ideal model delta sigma weight residual 118.90 117.20 1.70 9.40e-01 1.13e+00 3.28e+00 angle pdb=" CA VAL R 75 " pdb=" C VAL R 75 " pdb=" O VAL R 75 " ideal model delta sigma weight residual 118.90 120.45 -1.55 8.80e-01 1.29e+00 3.11e+00 angle pdb=" C LEU B 79 " pdb=" N ILE B 80 " pdb=" CA ILE B 80 " ideal model delta sigma weight residual 122.90 120.65 2.25 1.28e+00 6.10e-01 3.09e+00 ... (remaining 11223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 4466 17.29 - 34.57: 394 34.57 - 51.86: 89 51.86 - 69.14: 13 69.14 - 86.43: 4 Dihedral angle restraints: 4966 sinusoidal: 1950 harmonic: 3016 Sorted by residual: dihedral pdb=" CB CYS R 298 " pdb=" SG CYS R 298 " pdb=" SG CYS R 307 " pdb=" CB CYS R 307 " ideal model delta sinusoidal sigma weight residual 93.00 32.63 60.37 1 1.00e+01 1.00e-02 4.85e+01 dihedral pdb=" CA ASP B 212 " pdb=" CB ASP B 212 " pdb=" CG ASP B 212 " pdb=" OD1 ASP B 212 " ideal model delta sinusoidal sigma weight residual -30.00 -82.75 52.75 1 2.00e+01 2.50e-03 9.47e+00 dihedral pdb=" CB MET B 217 " pdb=" CG MET B 217 " pdb=" SD MET B 217 " pdb=" CE MET B 217 " ideal model delta sinusoidal sigma weight residual -180.00 -122.55 -57.45 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 4963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1090 0.055 - 0.109: 178 0.109 - 0.164: 10 0.164 - 0.219: 0 0.219 - 0.273: 1 Chirality restraints: 1279 Sorted by residual: chirality pdb=" C07 G3C R 501 " pdb=" C06 G3C R 501 " pdb=" C08 G3C R 501 " pdb=" C15 G3C R 501 " both_signs ideal model delta sigma weight residual False -2.44 -2.71 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA VAL B 296 " pdb=" N VAL B 296 " pdb=" C VAL B 296 " pdb=" CB VAL B 296 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 1276 not shown) Planarity restraints: 1418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 114 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C LEU R 114 " 0.024 2.00e-02 2.50e+03 pdb=" O LEU R 114 " -0.009 2.00e-02 2.50e+03 pdb=" N CYS R 115 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 104 " -0.007 2.00e-02 2.50e+03 1.35e-02 1.81e+00 pdb=" C ILE R 104 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE R 104 " -0.009 2.00e-02 2.50e+03 pdb=" N MET R 105 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE R 205 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO R 206 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO R 206 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 206 " -0.019 5.00e-02 4.00e+02 ... (remaining 1415 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 433 2.72 - 3.27: 8610 3.27 - 3.81: 14852 3.81 - 4.36: 18257 4.36 - 4.90: 30212 Nonbonded interactions: 72364 Sorted by model distance: nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.178 2.440 nonbonded pdb=" OG SER R 199 " pdb=" ND2 ASN R 292 " model vdw 2.179 2.520 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.186 2.440 nonbonded pdb=" CG1 VAL B 200 " pdb=" CE2 PHE B 234 " model vdw 2.200 3.760 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.222 2.440 ... (remaining 72359 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.000 Extract box with map and model: 2.740 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.890 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 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 : 0.002 0.054 8274 Z= 0.161 Angle : 0.480 5.340 11228 Z= 0.288 Chirality : 0.039 0.273 1279 Planarity : 0.003 0.033 1418 Dihedral : 13.674 86.426 2994 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.74 % Allowed : 12.33 % Favored : 85.93 % 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: -3.30 (0.23), residues: 1015 helix: -1.57 (0.22), residues: 383 sheet: -2.85 (0.32), residues: 188 loop : -2.31 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.001 0.000 HIS B 183 PHE 0.006 0.001 PHE B 235 TYR 0.009 0.001 TYR N 117 ARG 0.005 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 276 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.4469 (t80) cc_final: 0.3946 (t80) REVERT: B 150 ARG cc_start: 0.8555 (mmt-90) cc_final: 0.6648 (mmt90) REVERT: B 313 ASN cc_start: 0.8331 (t0) cc_final: 0.7938 (t0) REVERT: N 32 TYR cc_start: 0.8558 (m-80) cc_final: 0.8277 (m-80) REVERT: N 35 ASN cc_start: 0.7138 (p0) cc_final: 0.6920 (p0) REVERT: R 105 MET cc_start: 0.6811 (ttp) cc_final: 0.6604 (tmm) REVERT: R 125 ILE cc_start: 0.8110 (mm) cc_final: 0.7607 (mm) REVERT: R 154 ILE cc_start: 0.8044 (tp) cc_final: 0.7782 (tp) outliers start: 15 outliers final: 5 residues processed: 286 average time/residue: 0.2585 time to fit residues: 93.7886 Evaluate side-chains 217 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 212 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain R residue 136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 0.4980 chunk 91 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 278 ASN A 371 ASN A 390 GLN B 32 GLN B 125 ASN B 266 HIS B 340 ASN G 18 GLN N 84 ASN N 120 GLN N 123 GLN R 60 ASN R 323 ASN ** R 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8274 Z= 0.212 Angle : 0.518 6.686 11228 Z= 0.269 Chirality : 0.042 0.175 1279 Planarity : 0.004 0.051 1418 Dihedral : 5.032 41.077 1208 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.84 % Allowed : 18.02 % Favored : 78.14 % 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: -2.12 (0.25), residues: 1015 helix: -0.33 (0.25), residues: 393 sheet: -2.53 (0.33), residues: 187 loop : -1.78 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS B 266 PHE 0.027 0.001 PHE B 241 TYR 0.011 0.001 TYR B 124 ARG 0.006 0.001 ARG A 374 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 238 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 222 PHE cc_start: 0.4781 (t80) cc_final: 0.3806 (t80) REVERT: A 266 LEU cc_start: 0.9044 (tp) cc_final: 0.8813 (tp) REVERT: A 292 ASN cc_start: 0.7843 (OUTLIER) cc_final: 0.7629 (t0) REVERT: B 111 TYR cc_start: 0.7839 (m-80) cc_final: 0.7327 (m-80) REVERT: B 150 ARG cc_start: 0.8630 (mmt-90) cc_final: 0.8389 (mmt-90) REVERT: N 32 TYR cc_start: 0.8720 (m-80) cc_final: 0.8482 (m-80) REVERT: N 33 LYS cc_start: 0.8451 (tttm) cc_final: 0.8192 (tttm) REVERT: R 105 MET cc_start: 0.6894 (ttp) cc_final: 0.6686 (tmm) REVERT: R 114 LEU cc_start: 0.8077 (mt) cc_final: 0.7842 (mt) REVERT: R 125 ILE cc_start: 0.8406 (mm) cc_final: 0.7766 (mm) REVERT: R 154 ILE cc_start: 0.8065 (tp) cc_final: 0.7841 (tp) REVERT: R 199 SER cc_start: 0.8677 (OUTLIER) cc_final: 0.8183 (t) outliers start: 33 outliers final: 14 residues processed: 260 average time/residue: 0.2193 time to fit residues: 75.6997 Evaluate side-chains 234 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 218 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 120 GLN Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 199 SER Chi-restraints excluded: chain R residue 231 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN A 390 GLN B 237 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8274 Z= 0.255 Angle : 0.539 8.934 11228 Z= 0.277 Chirality : 0.041 0.140 1279 Planarity : 0.004 0.038 1418 Dihedral : 4.672 43.618 1206 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.95 % Allowed : 20.23 % Favored : 75.81 % 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: -1.66 (0.26), residues: 1015 helix: 0.07 (0.26), residues: 393 sheet: -2.38 (0.34), residues: 189 loop : -1.48 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 297 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE B 241 TYR 0.013 0.002 TYR N 60 ARG 0.009 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2030 Ramachandran restraints generated. 1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 234 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.4896 (t80) cc_final: 0.4339 (t80) REVERT: A 266 LEU cc_start: 0.9065 (tp) cc_final: 0.8759 (tp) REVERT: A 270 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8686 (mp) REVERT: A 318 TYR cc_start: 0.7102 (t80) cc_final: 0.6883 (t80) REVERT: B 111 TYR cc_start: 0.7925 (m-80) cc_final: 0.7635 (m-80) REVERT: B 150 ARG cc_start: 0.8728 (mmt-90) cc_final: 0.8405 (mmt-90) REVERT: R 154 ILE cc_start: 0.8188 (tp) cc_final: 0.7967 (tp) outliers start: 34 outliers final: 21 residues processed: 255 average time/residue: 0.2062 time to fit residues: 70.1164 Evaluate side-chains 245 residues out of total 891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 223 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 18 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 26 THR Chi-restraints excluded: chain R residue 34 ILE Chi-restraints excluded: chain R residue 136 THR Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 231 LEU 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: 70.0112 > 50: distance: 6 - 11: 6.613 distance: 11 - 12: 6.137 distance: 12 - 13: 14.432 distance: 12 - 15: 21.739 distance: 13 - 14: 8.627 distance: 13 - 19: 9.909 distance: 15 - 16: 5.421 distance: 16 - 17: 20.118 distance: 16 - 18: 20.337 distance: 19 - 20: 13.368 distance: 20 - 21: 26.309 distance: 20 - 23: 13.612 distance: 21 - 22: 22.468 distance: 21 - 25: 3.065 distance: 22 - 42: 14.967 distance: 23 - 24: 9.791 distance: 25 - 26: 15.260 distance: 26 - 27: 9.353 distance: 26 - 29: 9.092 distance: 27 - 34: 6.030 distance: 29 - 30: 30.665 distance: 30 - 31: 18.947 distance: 31 - 32: 11.010 distance: 31 - 33: 12.798 distance: 34 - 35: 24.820 distance: 35 - 36: 15.680 distance: 35 - 38: 44.636 distance: 36 - 37: 9.233 distance: 36 - 42: 11.718 distance: 37 - 57: 25.957 distance: 38 - 39: 9.520 distance: 38 - 40: 21.980 distance: 39 - 41: 6.629 distance: 42 - 43: 18.334 distance: 43 - 44: 17.456 distance: 43 - 46: 7.173 distance: 44 - 49: 15.752 distance: 46 - 47: 18.937 distance: 46 - 48: 38.645 distance: 49 - 50: 11.800 distance: 50 - 51: 46.414 distance: 50 - 53: 34.567 distance: 51 - 52: 9.382 distance: 51 - 57: 15.304 distance: 53 - 54: 40.699 distance: 54 - 56: 39.770 distance: 57 - 58: 23.554 distance: 58 - 59: 21.630 distance: 58 - 61: 40.845 distance: 59 - 60: 18.342 distance: 59 - 65: 3.173 distance: 61 - 62: 39.194 distance: 62 - 63: 35.936 distance: 65 - 66: 7.028 distance: 66 - 67: 26.533 distance: 66 - 69: 46.854 distance: 67 - 68: 11.596 distance: 67 - 73: 64.051 distance: 69 - 70: 16.552 distance: 69 - 71: 33.398 distance: 70 - 72: 24.367 distance: 73 - 74: 17.883 distance: 74 - 75: 3.591 distance: 74 - 77: 12.539 distance: 75 - 76: 10.686 distance: 75 - 81: 5.934 distance: 77 - 78: 7.317 distance: 78 - 79: 17.579 distance: 78 - 80: 9.108 distance: 81 - 82: 22.926 distance: 81 - 87: 7.662 distance: 82 - 83: 19.610 distance: 82 - 85: 13.872 distance: 83 - 84: 18.394 distance: 83 - 88: 8.466 distance: 85 - 86: 6.321 distance: 86 - 87: 41.703