Starting phenix.real_space_refine on Tue May 7 02:26:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ged_29966/05_2024/8ged_29966_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ged_29966/05_2024/8ged_29966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ged_29966/05_2024/8ged_29966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ged_29966/05_2024/8ged_29966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ged_29966/05_2024/8ged_29966_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ged_29966/05_2024/8ged_29966_updated.pdb" } resolution = 3.5 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= -0.001 sd= 0.028 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 37 5.16 5 C 4179 2.51 5 N 1142 2.21 5 O 1147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 107": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 6505 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1885 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'PTRANS': 6, 'TRANS': 274} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 444 Unresolved non-hydrogen angles: 544 Unresolved non-hydrogen dihedrals: 352 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 14, 'PHE:plan': 2, 'GLU:plan': 20, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 271 Chain: "B" Number of atoms: 2332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2332 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 6, 'ASP:plan': 17, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 182 Chain: "G" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 301 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "R" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1972 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 93} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 292 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 115 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.26, per 1000 atoms: 0.65 Number of scatterers: 6505 At special positions: 0 Unit cell: (71.02, 97.52, 126.14, 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 37 16.00 O 1147 8.00 N 1142 7.00 C 4179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " 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: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1794 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 8 sheets defined 45.3% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 13 through 39 removed outlier: 3.651A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 89 through 112 Processing helix chain 'A' and resid 161 through 167 removed outlier: 4.201A pdb=" N ARG A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ASN A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 250 through 253 removed outlier: 3.909A pdb=" N TYR A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 250 through 253' Processing helix chain 'A' and resid 265 through 277 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 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 8 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.265A 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 'G' and resid 14 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 32 through 60 removed outlier: 3.900A pdb=" N MET R 36 " --> pdb=" O TRP R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 95 removed outlier: 4.345A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 103 through 136 Processing helix chain 'R' and resid 141 through 144 No H-bonds generated for 'chain 'R' and resid 141 through 144' Processing helix chain 'R' and resid 147 through 163 Processing helix chain 'R' and resid 166 through 170 Processing helix chain 'R' and resid 182 through 186 Processing helix chain 'R' and resid 197 through 207 removed outlier: 3.934A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 236 removed outlier: 3.600A pdb=" N VAL R 222 " --> pdb=" O VAL R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 298 removed outlier: 3.906A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 3.970A pdb=" N VAL R 297 " --> pdb=" O ASN R 293 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 302 No H-bonds generated for 'chain 'R' and resid 300 through 302' Processing helix chain 'R' and resid 305 through 326 removed outlier: 3.830A pdb=" N SER R 319 " --> pdb=" O GLY R 315 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 339 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 3.927A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU A 44 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.522A pdb=" N TYR B 59 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.780A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.253A 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: 6.516A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.735A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.284A 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: 6.302A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.915A 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: 6.586A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 7.410A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 1035 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: 1.93 Time building geometry restraints manager: 2.81 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: 2140 1.34 - 1.46: 1724 1.46 - 1.58: 2732 1.58 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 6644 Sorted by residual: bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.580 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.453 -0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " ideal model delta sigma weight residual 1.520 1.570 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" CAD G1I R 501 " pdb=" CAE G1I R 501 " ideal model delta sigma weight residual 1.394 1.442 -0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" CAI G1I R 501 " pdb=" NAN G1I R 501 " ideal model delta sigma weight residual 1.451 1.492 -0.041 2.00e-02 2.50e+03 4.26e+00 ... (remaining 6639 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.03: 128 107.03 - 113.78: 3717 113.78 - 120.53: 2539 120.53 - 127.28: 2656 127.28 - 134.02: 74 Bond angle restraints: 9114 Sorted by residual: angle pdb=" CA LEU A 46 " pdb=" CB LEU A 46 " pdb=" CG LEU A 46 " ideal model delta sigma weight residual 116.30 125.02 -8.72 3.50e+00 8.16e-02 6.21e+00 angle pdb=" N CYS B 233 " pdb=" CA CYS B 233 " pdb=" C CYS B 233 " ideal model delta sigma weight residual 108.46 111.90 -3.44 1.51e+00 4.39e-01 5.19e+00 angle pdb=" CB LEU A 46 " pdb=" CG LEU A 46 " pdb=" CD2 LEU A 46 " ideal model delta sigma weight residual 110.70 104.13 6.57 3.00e+00 1.11e-01 4.79e+00 angle pdb=" N ASP B 258 " pdb=" CA ASP B 258 " pdb=" C ASP B 258 " ideal model delta sigma weight residual 113.56 110.67 2.89 1.39e+00 5.18e-01 4.32e+00 angle pdb=" N GLY B 244 " pdb=" CA GLY B 244 " pdb=" C GLY B 244 " ideal model delta sigma weight residual 113.02 110.05 2.97 1.59e+00 3.96e-01 3.50e+00 ... (remaining 9109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.10: 3438 14.10 - 28.20: 260 28.20 - 42.30: 92 42.30 - 56.40: 15 56.40 - 70.50: 5 Dihedral angle restraints: 3810 sinusoidal: 1049 harmonic: 2761 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 163.22 16.78 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ARG B 68 " pdb=" C ARG B 68 " pdb=" N LEU B 69 " pdb=" CA LEU B 69 " ideal model delta harmonic sigma weight residual -180.00 -163.89 -16.11 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA THR B 65 " pdb=" C THR B 65 " pdb=" N ASP B 66 " pdb=" CA ASP B 66 " ideal model delta harmonic sigma weight residual 180.00 164.10 15.90 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 3807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 798 0.037 - 0.075: 224 0.075 - 0.112: 64 0.112 - 0.150: 11 0.150 - 0.187: 2 Chirality restraints: 1099 Sorted by residual: chirality pdb=" CG LEU A 46 " pdb=" CB LEU A 46 " pdb=" CD1 LEU A 46 " pdb=" CD2 LEU A 46 " both_signs ideal model delta sigma weight residual False -2.59 -2.78 0.19 2.00e-01 2.50e+01 8.74e-01 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.56 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 ... (remaining 1096 not shown) Planarity restraints: 1163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 277 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C ILE R 277 " 0.022 2.00e-02 2.50e+03 pdb=" O ILE R 277 " -0.008 2.00e-02 2.50e+03 pdb=" N ILE R 278 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO B 236 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 233 " -0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C LYS A 233 " 0.018 2.00e-02 2.50e+03 pdb=" O LYS A 233 " -0.007 2.00e-02 2.50e+03 pdb=" N TRP A 234 " -0.006 2.00e-02 2.50e+03 ... (remaining 1160 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1403 2.78 - 3.31: 6329 3.31 - 3.84: 10934 3.84 - 4.37: 11410 4.37 - 4.90: 20850 Nonbonded interactions: 50926 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.251 2.440 nonbonded pdb=" O GLY B 224 " pdb=" NH1 ARG B 251 " model vdw 2.332 2.520 nonbonded pdb=" OG1 THR B 249 " pdb=" OG1 THR B 263 " model vdw 2.338 2.440 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.347 2.440 nonbonded pdb=" OG SER B 201 " pdb=" NE1 TRP B 211 " model vdw 2.364 2.520 ... (remaining 50921 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 5.860 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.810 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 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 : 0.003 0.057 6644 Z= 0.177 Angle : 0.475 8.721 9114 Z= 0.252 Chirality : 0.039 0.187 1099 Planarity : 0.003 0.031 1163 Dihedral : 12.401 70.496 2010 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: 1.82 (0.28), residues: 928 helix: 2.97 (0.25), residues: 415 sheet: -0.04 (0.42), residues: 147 loop : -0.34 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 277 HIS 0.004 0.001 HIS A 357 PHE 0.008 0.001 PHE R 133 TYR 0.006 0.001 TYR B 105 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.759 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1456 time to fit residues: 22.7057 Evaluate side-chains 81 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN R 312 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.0903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6644 Z= 0.225 Angle : 0.477 6.039 9114 Z= 0.255 Chirality : 0.041 0.154 1099 Planarity : 0.003 0.029 1163 Dihedral : 4.132 23.266 1013 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.38 % Allowed : 12.43 % Favored : 86.19 % 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: 1.94 (0.28), residues: 928 helix: 2.87 (0.25), residues: 430 sheet: -0.03 (0.41), residues: 157 loop : -0.12 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE R 193 TYR 0.011 0.001 TYR R 199 ARG 0.006 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 86 time to evaluate : 0.793 Fit side-chains revert: symmetry clash REVERT: B 237 ASN cc_start: 0.8396 (t0) cc_final: 0.8092 (t0) REVERT: R 82 MET cc_start: 0.6311 (ttm) cc_final: 0.6094 (ttp) outliers start: 7 outliers final: 6 residues processed: 90 average time/residue: 0.1222 time to fit residues: 17.0948 Evaluate side-chains 83 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain R residue 111 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 76 optimal weight: 0.0570 chunk 84 optimal weight: 0.0970 chunk 29 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 237 ASN B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6644 Z= 0.150 Angle : 0.427 5.771 9114 Z= 0.230 Chirality : 0.039 0.145 1099 Planarity : 0.003 0.030 1163 Dihedral : 3.796 16.778 1013 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.97 % Allowed : 14.79 % Favored : 83.23 % 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: 2.07 (0.28), residues: 928 helix: 2.93 (0.25), residues: 429 sheet: 0.39 (0.42), residues: 152 loop : -0.17 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE B 199 TYR 0.008 0.001 TYR R 199 ARG 0.004 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: B 262 MET cc_start: 0.6285 (tpp) cc_final: 0.6016 (tpt) outliers start: 10 outliers final: 8 residues processed: 93 average time/residue: 0.1156 time to fit residues: 16.6073 Evaluate side-chains 85 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 77 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 167 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.4980 chunk 64 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 chunk 40 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6644 Z= 0.186 Angle : 0.445 6.513 9114 Z= 0.239 Chirality : 0.040 0.142 1099 Planarity : 0.003 0.030 1163 Dihedral : 3.893 19.985 1013 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.96 % Allowed : 14.79 % Favored : 82.25 % 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: 1.96 (0.28), residues: 928 helix: 2.81 (0.25), residues: 427 sheet: 0.05 (0.39), residues: 164 loop : 0.01 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.007 0.001 HIS B 142 PHE 0.012 0.001 PHE B 199 TYR 0.009 0.001 TYR R 199 ARG 0.003 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 88 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: B 45 MET cc_start: 0.7965 (mmt) cc_final: 0.7597 (mmt) outliers start: 15 outliers final: 14 residues processed: 97 average time/residue: 0.1181 time to fit residues: 17.7929 Evaluate side-chains 99 residues out of total 818 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 111 SER Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-dev-5322/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-dev-5322/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-5322/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-5322/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-5322/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-5322/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-5322/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-5322/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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-5322/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-5322/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-dev-5322/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-dev-5322/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: 50.5227 > 50: distance: 95 - 101: 5.070 distance: 101 - 102: 3.860 distance: 102 - 103: 7.647 distance: 102 - 105: 7.589 distance: 103 - 104: 14.210 distance: 103 - 112: 10.920 distance: 105 - 106: 6.042 distance: 106 - 107: 6.211 distance: 107 - 108: 11.499 distance: 108 - 109: 8.485 distance: 109 - 110: 16.742 distance: 109 - 111: 6.517 distance: 112 - 113: 12.050 distance: 113 - 114: 13.627 distance: 113 - 116: 4.164 distance: 114 - 115: 29.325 distance: 114 - 118: 25.063 distance: 116 - 117: 8.054 distance: 118 - 119: 7.727 distance: 119 - 120: 4.507 distance: 119 - 122: 23.598 distance: 120 - 121: 3.473 distance: 120 - 124: 7.255 distance: 122 - 123: 8.181 distance: 124 - 125: 5.089 distance: 125 - 128: 4.020 distance: 126 - 127: 12.623 distance: 128 - 129: 4.592 distance: 129 - 131: 3.544 distance: 134 - 136: 3.557 distance: 135 - 137: 3.889 distance: 136 - 137: 5.080 distance: 139 - 140: 3.392 distance: 140 - 141: 3.744 distance: 140 - 145: 3.075 distance: 142 - 143: 6.487 distance: 142 - 144: 5.373 distance: 145 - 146: 3.937 distance: 146 - 147: 6.891 distance: 146 - 149: 9.385 distance: 147 - 148: 6.343 distance: 147 - 153: 4.373 distance: 149 - 150: 5.872 distance: 150 - 151: 8.893 distance: 151 - 152: 18.233 distance: 154 - 155: 4.038 distance: 155 - 156: 6.952 distance: 155 - 160: 5.573 distance: 157 - 158: 5.391 distance: 157 - 159: 5.097 distance: 160 - 161: 4.957 distance: 161 - 162: 3.922 distance: 161 - 164: 9.375 distance: 162 - 163: 4.043 distance: 162 - 166: 3.690 distance: 164 - 165: 7.139 distance: 166 - 207: 5.992 distance: 167 - 168: 5.121 distance: 167 - 170: 5.118 distance: 168 - 169: 3.185 distance: 168 - 171: 4.483 distance: 169 - 204: 8.749 distance: 171 - 172: 6.386 distance: 172 - 173: 3.846 distance: 172 - 175: 5.446 distance: 173 - 174: 8.884 distance: 173 - 183: 3.371 distance: 175 - 176: 5.433 distance: 176 - 177: 4.377 distance: 176 - 178: 6.221 distance: 177 - 179: 4.257 distance: 178 - 180: 3.086 distance: 179 - 181: 11.870 distance: 180 - 181: 13.165 distance: 181 - 182: 9.164