Starting phenix.real_space_refine on Fri Jan 17 05:30:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tr0_26077/01_2025/7tr0_26077.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tr0_26077/01_2025/7tr0_26077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tr0_26077/01_2025/7tr0_26077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tr0_26077/01_2025/7tr0_26077.map" model { file = "/net/cci-nas-00/data/ceres_data/7tr0_26077/01_2025/7tr0_26077.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tr0_26077/01_2025/7tr0_26077.cif" } resolution = 2.7 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6146 2.51 5 N 1706 2.21 5 O 1909 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9833 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3437 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain: "B" Number of atoms: 3376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3376 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "K" Number of atoms: 2866 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 360, 2843 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 360, 2843 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 14, 'TRANS': 345} Chain breaks: 1 bond proxies already assigned to first conformer: 2855 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.36, per 1000 atoms: 0.85 Number of scatterers: 9833 At special positions: 0 Unit cell: (70.55, 107.9, 110.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 8 15.00 Mg 1 11.99 O 1909 8.00 N 1706 7.00 C 6146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.7 seconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2300 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 9 sheets defined 48.9% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 36 through 42 removed outlier: 4.155A pdb=" N LYS A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.859A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 removed outlier: 3.642A pdb=" N GLY A 106 " --> pdb=" O ASN A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 113 removed outlier: 3.680A pdb=" N GLU A 113 " --> pdb=" O ILE A 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 110 through 113' Processing helix chain 'A' and resid 114 through 128 removed outlier: 3.567A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.892A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 190 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 239 removed outlier: 3.880A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 Processing helix chain 'A' and resid 251 through 260 Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.887A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.759A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.216A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.978A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 435 removed outlier: 4.081A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG A 422 " --> pdb=" O PHE A 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 46 removed outlier: 4.090A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.598A pdb=" N ILE B 84 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 85 " --> pdb=" O GLY B 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 81 through 85' Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 108 through 126 removed outlier: 4.024A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 126 " --> pdb=" O LYS B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 193 removed outlier: 3.700A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.531A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 241 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.616A pdb=" N MET B 299 " --> pdb=" O SER B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 Processing helix chain 'B' and resid 374 through 390 removed outlier: 3.716A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.892A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 43 removed outlier: 3.960A pdb=" N LEU K 43 " --> pdb=" O GLU K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 47 Processing helix chain 'K' and resid 124 through 132 removed outlier: 3.586A pdb=" N GLN K 128 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN K 130 " --> pdb=" O LYS K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 166 removed outlier: 3.561A pdb=" N VAL K 161 " --> pdb=" O THR K 157 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 176 removed outlier: 3.714A pdb=" N LEU K 170 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP K 171 " --> pdb=" O GLN K 167 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER K 172 " --> pdb=" O PRO K 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 196 Processing helix chain 'K' and resid 203 through 219 Processing helix chain 'K' and resid 274 through 287 Processing helix chain 'K' and resid 339 through 343 Processing helix chain 'K' and resid 347 through 372 removed outlier: 3.938A pdb=" N ASN K 351 " --> pdb=" O GLY K 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 378 removed outlier: 3.785A pdb=" N ASN K 377 " --> pdb=" O ARG K 374 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HIS K 378 " --> pdb=" O ARG K 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 374 through 378' Processing helix chain 'K' and resid 380 through 383 removed outlier: 3.671A pdb=" N ASP K 383 " --> pdb=" O PRO K 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 380 through 383' Processing helix chain 'K' and resid 384 through 390 Processing helix chain 'K' and resid 391 through 394 removed outlier: 4.311A pdb=" N LEU K 394 " --> pdb=" O LYS K 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 391 through 394' Processing helix chain 'K' and resid 409 through 411 No H-bonds generated for 'chain 'K' and resid 409 through 411' Processing helix chain 'K' and resid 412 through 426 removed outlier: 4.071A pdb=" N ALA K 426 " --> pdb=" O TYR K 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 removed outlier: 8.012A pdb=" N LEU A 92 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE A 67 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N HIS A 139 " --> pdb=" O ILE A 171 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 269 through 272 removed outlier: 6.668A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.129A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.811A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA6, first strand: chain 'K' and resid 150 through 152 removed outlier: 6.353A pdb=" N THR K 180 " --> pdb=" O VAL K 401 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ILE K 403 " --> pdb=" O THR K 180 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N PHE K 182 " --> pdb=" O ILE K 403 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N CYS K 405 " --> pdb=" O PHE K 182 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR K 184 " --> pdb=" O CYS K 405 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA K 179 " --> pdb=" O SER K 330 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ILE K 332 " --> pdb=" O ALA K 179 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL K 181 " --> pdb=" O ILE K 332 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 106 through 110 removed outlier: 3.866A pdb=" N VAL K 109 " --> pdb=" O MET K 113 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET K 113 " --> pdb=" O VAL K 109 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 254 through 256 Processing sheet with id=AA9, first strand: chain 'K' and resid 291 through 292 removed outlier: 3.790A pdb=" N SER K 300 " --> pdb=" O SER K 292 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1276 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: 2.90 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1752 1.32 - 1.45: 2579 1.45 - 1.57: 5590 1.57 - 1.69: 21 1.69 - 1.81: 98 Bond restraints: 10040 Sorted by residual: bond pdb=" N3B ANP K 501 " pdb=" PG ANP K 501 " ideal model delta sigma weight residual 1.795 1.633 0.162 2.00e-02 2.50e+03 6.55e+01 bond pdb=" C ARG K 240 " pdb=" O ARG K 240 " ideal model delta sigma weight residual 1.235 1.297 -0.062 1.19e-02 7.06e+03 2.72e+01 bond pdb=" O3A ANP K 501 " pdb=" PB ANP K 501 " ideal model delta sigma weight residual 1.700 1.600 0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" N GLU K 295 " pdb=" CA GLU K 295 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.16e-02 7.43e+03 7.10e+00 bond pdb=" O5' ANP K 501 " pdb=" PA ANP K 501 " ideal model delta sigma weight residual 1.655 1.604 0.051 2.00e-02 2.50e+03 6.46e+00 ... (remaining 10035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 13325 2.34 - 4.69: 256 4.69 - 7.03: 49 7.03 - 9.38: 5 9.38 - 11.72: 2 Bond angle restraints: 13637 Sorted by residual: angle pdb=" N ARG K 129 " pdb=" CA ARG K 129 " pdb=" C ARG K 129 " ideal model delta sigma weight residual 112.23 103.75 8.48 1.26e+00 6.30e-01 4.53e+01 angle pdb=" CB LYS K 430 " pdb=" CG LYS K 430 " pdb=" CD LYS K 430 " ideal model delta sigma weight residual 111.30 123.02 -11.72 2.30e+00 1.89e-01 2.60e+01 angle pdb=" O ARG K 240 " pdb=" C ARG K 240 " pdb=" CA BARG K 240 " ideal model delta sigma weight residual 120.25 126.00 -5.75 1.26e+00 6.30e-01 2.09e+01 angle pdb=" O ARG K 240 " pdb=" C ARG K 240 " pdb=" CA AARG K 240 " ideal model delta sigma weight residual 120.25 125.82 -5.57 1.26e+00 6.30e-01 1.96e+01 angle pdb=" N LEU K 242 " pdb=" CA LEU K 242 " pdb=" C LEU K 242 " ideal model delta sigma weight residual 113.41 108.34 5.07 1.22e+00 6.72e-01 1.73e+01 ... (remaining 13632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.14: 5862 30.14 - 60.28: 239 60.28 - 90.42: 29 90.42 - 120.56: 1 120.56 - 150.70: 13 Dihedral angle restraints: 6144 sinusoidal: 2570 harmonic: 3574 Sorted by residual: dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -140.03 -150.70 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -37.46 142.05 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" O3B GTP A 501 " pdb=" O3A GTP A 501 " pdb=" PB GTP A 501 " pdb=" PA GTP A 501 " ideal model delta sinusoidal sigma weight residual 291.08 169.39 121.69 1 2.00e+01 2.50e-03 3.66e+01 ... (remaining 6141 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1193 0.052 - 0.104: 231 0.104 - 0.156: 86 0.156 - 0.208: 2 0.208 - 0.260: 2 Chirality restraints: 1514 Sorted by residual: chirality pdb=" C3' ANP K 501 " pdb=" C2' ANP K 501 " pdb=" C4' ANP K 501 " pdb=" O3' ANP K 501 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ARG K 129 " pdb=" N ARG K 129 " pdb=" C ARG K 129 " pdb=" CB ARG K 129 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR K 165 " pdb=" CA THR K 165 " pdb=" OG1 THR K 165 " pdb=" CG2 THR K 165 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.56e-01 ... (remaining 1511 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN K 128 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C GLN K 128 " -0.049 2.00e-02 2.50e+03 pdb=" O GLN K 128 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG K 129 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR K 422 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.20e+00 pdb=" C TYR K 422 " 0.031 2.00e-02 2.50e+03 pdb=" O TYR K 422 " -0.012 2.00e-02 2.50e+03 pdb=" N ALA K 423 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 88 " 0.030 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO A 89 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " 0.025 5.00e-02 4.00e+02 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 70 2.58 - 3.16: 8013 3.16 - 3.74: 14907 3.74 - 4.32: 21690 4.32 - 4.90: 37137 Nonbonded interactions: 81817 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 2.005 2.170 nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 2.121 2.170 nonbonded pdb=" O SER B 278 " pdb=" OG SER B 278 " model vdw 2.192 3.040 nonbonded pdb=" O TYR K 235 " pdb=" OG1 THR K 238 " model vdw 2.194 3.040 nonbonded pdb=" OH TYR K 162 " pdb=" OE1 GLU K 211 " model vdw 2.221 3.040 ... (remaining 81812 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=0.46 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: 12.030 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 26.690 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:12.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 10040 Z= 0.345 Angle : 0.815 11.724 13637 Z= 0.443 Chirality : 0.049 0.260 1514 Planarity : 0.005 0.054 1770 Dihedral : 18.003 150.698 3844 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.66 % Allowed : 12.27 % Favored : 87.08 % 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: -0.37 (0.24), residues: 1224 helix: 0.83 (0.24), residues: 486 sheet: -0.47 (0.33), residues: 230 loop : -1.14 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 21 HIS 0.005 0.001 HIS B 37 PHE 0.014 0.001 PHE A 149 TYR 0.021 0.001 TYR K 235 ARG 0.009 0.001 ARG K 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 221 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: K 244 ASN cc_start: 0.8480 (t0) cc_final: 0.8142 (t0) REVERT: K 349 ARG cc_start: 0.5922 (mmm-85) cc_final: 0.5450 (mtt180) REVERT: K 424 ASP cc_start: 0.7649 (t70) cc_final: 0.7443 (t0) outliers start: 7 outliers final: 5 residues processed: 228 average time/residue: 1.3610 time to fit residues: 333.0517 Evaluate side-chains 220 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 215 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain K residue 106 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 110 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 372 GLN B 6 HIS B 134 GLN K 130 ASN K 259 ASN K 288 ASN K 310 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.134450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.107780 restraints weight = 21944.075| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.48 r_work: 0.3281 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10040 Z= 0.235 Angle : 0.586 10.114 13637 Z= 0.286 Chirality : 0.045 0.255 1514 Planarity : 0.004 0.039 1770 Dihedral : 12.767 148.246 1520 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.50 % Allowed : 12.92 % Favored : 85.58 % 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: 0.25 (0.24), residues: 1224 helix: 1.39 (0.24), residues: 499 sheet: -0.30 (0.33), residues: 233 loop : -0.82 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 21 HIS 0.005 0.001 HIS B 137 PHE 0.011 0.001 PHE B 367 TYR 0.015 0.001 TYR A 103 ARG 0.004 0.000 ARG K 269 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 1.131 Fit side-chains revert: symmetry clash REVERT: A 308 ARG cc_start: 0.8523 (mtt90) cc_final: 0.8292 (mtm180) REVERT: K 288 ASN cc_start: 0.8395 (OUTLIER) cc_final: 0.8152 (t0) REVERT: K 349 ARG cc_start: 0.6312 (mmm-85) cc_final: 0.5910 (mtt-85) REVERT: K 424 ASP cc_start: 0.8264 (t70) cc_final: 0.8062 (t0) outliers start: 16 outliers final: 10 residues processed: 225 average time/residue: 1.2763 time to fit residues: 307.2933 Evaluate side-chains 223 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 288 ASN Chi-restraints excluded: chain K residue 307 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 256 GLN B 52 ASN B 307 HIS K 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.133714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106682 restraints weight = 24298.461| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.63 r_work: 0.3253 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3076 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10040 Z= 0.271 Angle : 0.565 8.916 13637 Z= 0.277 Chirality : 0.047 0.428 1514 Planarity : 0.004 0.041 1770 Dihedral : 9.996 145.791 1516 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.25 % Allowed : 13.30 % Favored : 84.46 % 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: 0.37 (0.24), residues: 1224 helix: 1.48 (0.24), residues: 496 sheet: -0.10 (0.33), residues: 230 loop : -0.80 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 21 HIS 0.005 0.001 HIS B 137 PHE 0.013 0.001 PHE A 149 TYR 0.016 0.001 TYR A 103 ARG 0.006 0.000 ARG K 269 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 1.057 Fit side-chains revert: symmetry clash REVERT: A 411 GLU cc_start: 0.8276 (mm-30) cc_final: 0.8020 (mm-30) REVERT: K 349 ARG cc_start: 0.6451 (mmm-85) cc_final: 0.6026 (mtt-85) REVERT: K 424 ASP cc_start: 0.8229 (t70) cc_final: 0.7993 (t0) outliers start: 24 outliers final: 14 residues processed: 224 average time/residue: 1.3092 time to fit residues: 313.2995 Evaluate side-chains 215 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 410 GLU Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain K residue 173 VAL Chi-restraints excluded: chain K residue 208 THR Chi-restraints excluded: chain K residue 221 ASP Chi-restraints excluded: chain K residue 233 GLU Chi-restraints excluded: chain K residue 287 LYS Chi-restraints excluded: chain K residue 307 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/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-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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-5571/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-5571/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-5571/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-5571/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: 53.9003 > 50: distance: 94 - 99: 28.573 distance: 99 - 100: 11.429 distance: 100 - 101: 11.535 distance: 100 - 103: 15.750 distance: 101 - 102: 16.442 distance: 101 - 110: 14.900 distance: 103 - 104: 4.737 distance: 104 - 105: 13.450 distance: 104 - 106: 16.654 distance: 105 - 107: 12.307 distance: 106 - 108: 27.763 distance: 107 - 109: 24.188 distance: 108 - 109: 3.263 distance: 110 - 111: 6.642 distance: 110 - 116: 22.299 distance: 111 - 112: 17.535 distance: 111 - 114: 15.002 distance: 112 - 113: 5.840 distance: 112 - 117: 17.915 distance: 114 - 115: 17.268 distance: 115 - 116: 18.391 distance: 117 - 118: 15.287 distance: 118 - 119: 13.119 distance: 118 - 121: 6.431 distance: 119 - 120: 16.752 distance: 119 - 128: 30.134 distance: 121 - 122: 14.828 distance: 122 - 123: 4.589 distance: 123 - 124: 14.638 distance: 124 - 125: 20.522 distance: 125 - 126: 4.486 distance: 125 - 127: 20.409 distance: 128 - 129: 10.757 distance: 129 - 130: 10.029 distance: 129 - 132: 15.654 distance: 130 - 131: 25.921 distance: 130 - 136: 18.485 distance: 132 - 133: 23.527 distance: 133 - 134: 24.711 distance: 133 - 135: 38.394 distance: 136 - 137: 37.411 distance: 137 - 138: 16.133 distance: 137 - 140: 14.753 distance: 138 - 139: 27.020 distance: 138 - 146: 8.268 distance: 140 - 141: 22.484 distance: 141 - 142: 15.888 distance: 141 - 143: 13.185 distance: 142 - 144: 8.704 distance: 143 - 145: 9.824 distance: 144 - 145: 20.432 distance: 146 - 147: 17.169 distance: 147 - 148: 13.231 distance: 147 - 150: 12.506 distance: 148 - 149: 16.045 distance: 148 - 157: 23.109 distance: 150 - 151: 11.341 distance: 151 - 152: 23.804 distance: 151 - 153: 21.103 distance: 152 - 154: 6.889 distance: 153 - 155: 11.851 distance: 154 - 156: 35.412 distance: 155 - 156: 19.054 distance: 157 - 158: 6.184 distance: 158 - 159: 14.940 distance: 158 - 161: 10.698 distance: 159 - 160: 13.197 distance: 159 - 168: 17.909 distance: 161 - 162: 5.470 distance: 162 - 163: 16.311 distance: 162 - 164: 4.246 distance: 163 - 165: 8.294 distance: 164 - 166: 25.292 distance: 165 - 167: 3.715 distance: 166 - 167: 12.505 distance: 168 - 169: 5.966 distance: 168 - 253: 14.256 distance: 169 - 170: 20.116 distance: 169 - 172: 22.753 distance: 170 - 171: 10.436 distance: 170 - 176: 8.472 distance: 171 - 250: 9.597 distance: 172 - 173: 7.070 distance: 173 - 174: 17.461 distance: 174 - 175: 10.396 distance: 176 - 177: 14.225 distance: 176 - 182: 26.427 distance: 177 - 178: 18.903 distance: 177 - 180: 15.640 distance: 178 - 179: 25.371 distance: 178 - 183: 23.694 distance: 180 - 181: 18.420 distance: 181 - 182: 3.018 distance: 183 - 184: 19.154 distance: 183 - 239: 17.613 distance: 184 - 185: 16.729 distance: 185 - 186: 25.195 distance: 185 - 187: 15.567 distance: 186 - 236: 11.947