Starting phenix.real_space_refine on Thu Jan 23 15:05:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tt1_26107/01_2025/7tt1_26107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tt1_26107/01_2025/7tt1_26107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tt1_26107/01_2025/7tt1_26107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tt1_26107/01_2025/7tt1_26107.map" model { file = "/net/cci-nas-00/data/ceres_data/7tt1_26107/01_2025/7tt1_26107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tt1_26107/01_2025/7tt1_26107.cif" } resolution = 4.3 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= 0.007 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 6558 2.51 5 N 1773 2.21 5 O 2030 1.98 5 H 10005 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 20398 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 287 Classifications: {'peptide': 18} Modifications used: {'COO': 1} Link IDs: {'TRANS': 17} Chain breaks: 1 Chain: "A" Number of atoms: 9476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 9476 Classifications: {'peptide': 612} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 587} Chain breaks: 4 Chain: "B" Number of atoms: 5187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 5187 Classifications: {'peptide': 349} Link IDs: {'PTRANS': 11, 'TRANS': 337} Chain breaks: 2 Chain: "E" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1382 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "D" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3390 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 10, 'TRANS': 202} Chain: "C" Number of atoms: 676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 676 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 6, 'TRANS': 41} Time building chain proxies: 9.51, per 1000 atoms: 0.47 Number of scatterers: 20398 At special positions: 0 Unit cell: (113.825, 122.415, 137.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 2030 8.00 N 1773 7.00 C 6558 6.00 H 10005 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS P1299 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 690 " - pdb=" SG CYS A 700 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 1.5 seconds 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2422 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 15 sheets defined 23.8% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 218 through 232 removed outlier: 4.134A pdb=" N ASP A 222 " --> pdb=" O LYS A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 252 Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 297 through 316 Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.105A pdb=" N LEU A 365 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.823A pdb=" N VAL A 382 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'E' and resid 39 through 44 Processing helix chain 'E' and resid 51 through 60 Processing helix chain 'D' and resid 32 through 45 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.877A pdb=" N VAL D 108 " --> pdb=" O ASN D 104 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 131 through 135 removed outlier: 4.366A pdb=" N ASP D 134 " --> pdb=" O ASP D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 removed outlier: 3.782A pdb=" N ARG D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) Proline residue: D 216 - end of helix removed outlier: 3.765A pdb=" N GLU D 219 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN D 220 " --> pdb=" O PRO D 216 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.772A pdb=" N LYS D 233 " --> pdb=" O ALA D 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 44 removed outlier: 3.538A pdb=" N ALA C 44 " --> pdb=" O TYR C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing sheet with id=AA1, first strand: chain 'P' and resid 1272 through 1276 removed outlier: 3.784A pdb=" N ARG P1273 " --> pdb=" O ARG P1297 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY P1275 " --> pdb=" O ASN P1295 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN P1295 " --> pdb=" O GLY P1275 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 445 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE A 440 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASN A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 532 " --> pdb=" O ASP A 569 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP A 569 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 600 " --> pdb=" O TYR A 608 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 710 " --> pdb=" O TRP A 745 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET A 768 " --> pdb=" O PHE A 791 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 183 removed outlier: 4.061A pdb=" N GLN A 179 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER A 242 " --> pdb=" O ASN A 259 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 276 removed outlier: 6.525A pdb=" N LYS A 267 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU A 337 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N SER A 269 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 12.975A pdb=" N VAL A 339 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 10.287A pdb=" N VAL A 271 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 12.056A pdb=" N VAL A 341 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 9.800A pdb=" N VAL A 273 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 348 through 355 removed outlier: 6.267A pdb=" N TYR A 348 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL A 414 " --> pdb=" O TYR A 348 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ARG A 350 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 12.940A pdb=" N TYR A 416 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N ILE A 352 " --> pdb=" O TYR A 416 " (cutoff:3.500A) removed outlier: 12.554A pdb=" N VAL A 418 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 9.980A pdb=" N PHE A 354 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 11.845A pdb=" N GLU A 420 " --> pdb=" O PHE A 354 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 415 " --> pdb=" O ASP A 401 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 419 " --> pdb=" O THR A 397 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR A 397 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 671 through 674 removed outlier: 4.923A pdb=" N ASP A 704 " --> pdb=" O ALA A 672 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR A 674 " --> pdb=" O SER A 702 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N SER A 702 " --> pdb=" O TYR A 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.026A pdb=" N GLY B 385 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE B 380 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU B 378 " --> pdb=" O ILE B 390 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 68 removed outlier: 5.707A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 118 removed outlier: 6.268A pdb=" N GLY B 114 " --> pdb=" O GLY B 125 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLY B 125 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN B 130 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL B 131 " --> pdb=" O GLN B 144 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN B 144 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA B 133 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 156 through 157 removed outlier: 3.646A pdb=" N VAL B 156 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 201 through 203 removed outlier: 3.732A pdb=" N THR B 201 " --> pdb=" O VAL B 208 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TRP B 228 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 252 through 254 removed outlier: 3.566A pdb=" N ASN B 266 " --> pdb=" O ALA B 262 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP B 279 " --> pdb=" O ALA B 269 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.860A pdb=" N ILE B 290 " --> pdb=" O TYR B 297 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET B 306 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.738A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 32 through 35 removed outlier: 3.893A pdb=" N MET E 64 " --> pdb=" O PHE E 74 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 32 through 35 removed outlier: 6.825A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1299 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: 8.76 Time building geometry restraints manager: 5.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10005 1.03 - 1.23: 361 1.23 - 1.43: 4284 1.43 - 1.63: 5916 1.63 - 1.83: 60 Bond restraints: 20626 Sorted by residual: bond pdb=" CA PRO C 84 " pdb=" C PRO C 84 " ideal model delta sigma weight residual 1.514 1.522 -0.007 5.50e-03 3.31e+04 1.82e+00 bond pdb=" C THR B 43 " pdb=" O THR B 43 " ideal model delta sigma weight residual 1.235 1.229 0.006 4.70e-03 4.53e+04 1.58e+00 bond pdb=" CA TYR A 348 " pdb=" CB TYR A 348 " ideal model delta sigma weight residual 1.534 1.508 0.026 2.33e-02 1.84e+03 1.25e+00 bond pdb=" CB LEU E 63 " pdb=" CG LEU E 63 " ideal model delta sigma weight residual 1.530 1.509 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" C LEU A 365 " pdb=" N ARG A 366 " ideal model delta sigma weight residual 1.335 1.320 0.015 1.38e-02 5.25e+03 1.13e+00 ... (remaining 20621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 34703 1.32 - 2.65: 2103 2.65 - 3.97: 208 3.97 - 5.30: 29 5.30 - 6.62: 7 Bond angle restraints: 37050 Sorted by residual: angle pdb=" N MET D 225 " pdb=" CA MET D 225 " pdb=" C MET D 225 " ideal model delta sigma weight residual 109.76 103.34 6.42 1.64e+00 3.72e-01 1.53e+01 angle pdb=" N PHE A 738 " pdb=" CA PHE A 738 " pdb=" C PHE A 738 " ideal model delta sigma weight residual 109.07 114.32 -5.25 1.52e+00 4.33e-01 1.19e+01 angle pdb=" N PHE A 737 " pdb=" CA PHE A 737 " pdb=" C PHE A 737 " ideal model delta sigma weight residual 109.76 104.31 5.45 1.64e+00 3.72e-01 1.10e+01 angle pdb=" N ASP A 746 " pdb=" CA ASP A 746 " pdb=" C ASP A 746 " ideal model delta sigma weight residual 108.73 114.09 -5.36 1.63e+00 3.76e-01 1.08e+01 angle pdb=" N GLN D 224 " pdb=" CA GLN D 224 " pdb=" C GLN D 224 " ideal model delta sigma weight residual 111.82 108.01 3.81 1.16e+00 7.43e-01 1.08e+01 ... (remaining 37045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 9275 17.86 - 35.73: 303 35.73 - 53.59: 167 53.59 - 71.46: 49 71.46 - 89.32: 14 Dihedral angle restraints: 9808 sinusoidal: 5268 harmonic: 4540 Sorted by residual: dihedral pdb=" CA GLY A 482 " pdb=" C GLY A 482 " pdb=" N VAL A 483 " pdb=" CA VAL A 483 " ideal model delta harmonic sigma weight residual 180.00 159.04 20.96 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ILE A 519 " pdb=" C ILE A 519 " pdb=" N ASN A 520 " pdb=" CA ASN A 520 " ideal model delta harmonic sigma weight residual 180.00 159.45 20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CB CYS A 690 " pdb=" SG CYS A 690 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -118.74 32.74 1 1.00e+01 1.00e-02 1.53e+01 ... (remaining 9805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 921 0.032 - 0.063: 374 0.063 - 0.095: 162 0.095 - 0.127: 86 0.127 - 0.158: 21 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CA TYR A 585 " pdb=" N TYR A 585 " pdb=" C TYR A 585 " pdb=" CB TYR A 585 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE A 240 " pdb=" N ILE A 240 " pdb=" C ILE A 240 " pdb=" CB ILE A 240 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ILE A 806 " pdb=" N ILE A 806 " pdb=" C ILE A 806 " pdb=" CB ILE A 806 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 1561 not shown) Planarity restraints: 3157 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 86 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" C PRO D 86 " -0.053 2.00e-02 2.50e+03 pdb=" O PRO D 86 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU D 87 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 33 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.38e+00 pdb=" C ASN D 33 " -0.047 2.00e-02 2.50e+03 pdb=" O ASN D 33 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU D 34 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 544 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.36e+00 pdb=" C ALA A 544 " 0.036 2.00e-02 2.50e+03 pdb=" O ALA A 544 " -0.014 2.00e-02 2.50e+03 pdb=" N MET A 545 " -0.012 2.00e-02 2.50e+03 ... (remaining 3154 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.09: 441 2.09 - 2.72: 34873 2.72 - 3.35: 54979 3.35 - 3.97: 71350 3.97 - 4.60: 111354 Nonbonded interactions: 272997 Sorted by model distance: nonbonded pdb=" OD2 ASP A 624 " pdb=" HZ2 LYS A 626 " model vdw 1.466 2.450 nonbonded pdb=" OD1 ASP A 569 " pdb=" H ASP A 605 " model vdw 1.493 2.450 nonbonded pdb=" H ASN B 85 " pdb=" O LYS B 90 " model vdw 1.497 2.450 nonbonded pdb=" HG SER B 285 " pdb=" O VAL B 299 " model vdw 1.501 2.450 nonbonded pdb=" H ASN B 350 " pdb=" O ARG B 355 " model vdw 1.527 2.450 ... (remaining 272992 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=1.00 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: 0.990 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: 0.300 Extract box with map and model: 0.760 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 43.290 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10621 Z= 0.237 Angle : 0.817 6.619 14427 Z= 0.507 Chirality : 0.047 0.158 1564 Planarity : 0.004 0.037 1896 Dihedral : 10.413 89.321 3826 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.92 (0.22), residues: 1303 helix: 0.36 (0.28), residues: 284 sheet: 1.13 (0.25), residues: 384 loop : 0.56 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP D 191 HIS 0.009 0.002 HIS B 165 PHE 0.026 0.002 PHE A 586 TYR 0.016 0.003 TYR A 432 ARG 0.030 0.003 ARG A 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 1.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 HIS cc_start: 0.8289 (m-70) cc_final: 0.8029 (p90) REVERT: A 227 ARG cc_start: 0.8908 (mtp180) cc_final: 0.8527 (mtp85) REVERT: A 232 ASP cc_start: 0.8983 (m-30) cc_final: 0.8769 (m-30) REVERT: A 574 TYR cc_start: 0.8655 (p90) cc_final: 0.8411 (p90) REVERT: A 719 ILE cc_start: 0.8267 (mt) cc_final: 0.7832 (mt) REVERT: B 164 ILE cc_start: 0.9347 (mm) cc_final: 0.9141 (mp) REVERT: B 296 ILE cc_start: 0.9062 (mt) cc_final: 0.8764 (mt) REVERT: E 111 SER cc_start: 0.7751 (m) cc_final: 0.7516 (p) REVERT: D 58 LEU cc_start: 0.8090 (mt) cc_final: 0.7842 (mt) REVERT: D 60 ASN cc_start: 0.8521 (m-40) cc_final: 0.8157 (m110) REVERT: D 171 LYS cc_start: 0.8567 (mtpt) cc_final: 0.8360 (ttmm) REVERT: D 180 SER cc_start: 0.8788 (m) cc_final: 0.8407 (t) REVERT: D 198 VAL cc_start: 0.9434 (t) cc_final: 0.9081 (t) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.5835 time to fit residues: 302.1398 Evaluate side-chains 231 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN B 319 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.133531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093584 restraints weight = 69757.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.096386 restraints weight = 33237.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.097797 restraints weight = 21415.422| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10621 Z= 0.303 Angle : 0.629 5.752 14427 Z= 0.362 Chirality : 0.045 0.177 1564 Planarity : 0.005 0.042 1896 Dihedral : 5.224 87.090 1455 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: 0.77 (0.22), residues: 1303 helix: 1.23 (0.29), residues: 285 sheet: 0.56 (0.23), residues: 411 loop : 0.28 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 376 HIS 0.011 0.002 HIS A 533 PHE 0.022 0.002 PHE A 738 TYR 0.015 0.002 TYR D 154 ARG 0.005 0.001 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 271 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 HIS cc_start: 0.8941 (m90) cc_final: 0.8602 (m90) REVERT: A 232 ASP cc_start: 0.8879 (m-30) cc_final: 0.8639 (m-30) REVERT: A 371 GLN cc_start: 0.8108 (tp40) cc_final: 0.7628 (tp-100) REVERT: A 372 MET cc_start: 0.8717 (mpp) cc_final: 0.7466 (mpp) REVERT: A 408 SER cc_start: 0.8718 (t) cc_final: 0.8499 (m) REVERT: A 422 ASN cc_start: 0.8105 (m-40) cc_final: 0.7886 (m-40) REVERT: A 539 MET cc_start: 0.9171 (tpp) cc_final: 0.8780 (tpp) REVERT: A 785 PHE cc_start: 0.8817 (p90) cc_final: 0.8574 (p90) REVERT: B 76 ASP cc_start: 0.8517 (t0) cc_final: 0.8104 (t0) REVERT: B 123 TYR cc_start: 0.8641 (m-10) cc_final: 0.8364 (m-80) REVERT: B 270 LEU cc_start: 0.8907 (mt) cc_final: 0.8702 (mm) REVERT: B 278 MET cc_start: 0.7556 (mpp) cc_final: 0.7242 (mpp) REVERT: E 53 GLN cc_start: 0.9124 (mp10) cc_final: 0.8881 (mp10) REVERT: E 101 LEU cc_start: 0.9110 (tp) cc_final: 0.8895 (tt) REVERT: D 58 LEU cc_start: 0.8519 (mt) cc_final: 0.8191 (mt) REVERT: D 60 ASN cc_start: 0.8823 (m-40) cc_final: 0.8421 (m110) REVERT: D 79 TYR cc_start: 0.9186 (m-80) cc_final: 0.8634 (m-10) REVERT: D 89 GLN cc_start: 0.9216 (mt0) cc_final: 0.8580 (mm-40) REVERT: D 115 THR cc_start: 0.9255 (m) cc_final: 0.8916 (m) REVERT: D 116 ASN cc_start: 0.9301 (m-40) cc_final: 0.8971 (t0) REVERT: D 180 SER cc_start: 0.9169 (m) cc_final: 0.8944 (t) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.5603 time to fit residues: 210.3055 Evaluate side-chains 213 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 68 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 62 optimal weight: 0.0030 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 2 optimal weight: 0.4980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN D 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.136303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.103390 restraints weight = 70124.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.109839 restraints weight = 43027.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.109376 restraints weight = 27544.596| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10621 Z= 0.158 Angle : 0.531 4.419 14427 Z= 0.297 Chirality : 0.044 0.190 1564 Planarity : 0.004 0.080 1896 Dihedral : 5.035 87.812 1455 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 0.78 (0.22), residues: 1303 helix: 1.57 (0.30), residues: 285 sheet: 0.42 (0.23), residues: 405 loop : 0.21 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 739 HIS 0.007 0.001 HIS A 186 PHE 0.024 0.001 PHE A 426 TYR 0.011 0.001 TYR A 754 ARG 0.006 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1293 ASN cc_start: 0.8892 (t0) cc_final: 0.8404 (t0) REVERT: A 186 HIS cc_start: 0.8194 (p-80) cc_final: 0.7988 (p90) REVERT: A 232 ASP cc_start: 0.8913 (m-30) cc_final: 0.8653 (m-30) REVERT: A 371 GLN cc_start: 0.7342 (tp40) cc_final: 0.6901 (tp-100) REVERT: A 372 MET cc_start: 0.7547 (mpp) cc_final: 0.6992 (mpp) REVERT: A 539 MET cc_start: 0.8918 (tpp) cc_final: 0.8673 (tpp) REVERT: A 648 PHE cc_start: 0.8572 (p90) cc_final: 0.8254 (p90) REVERT: A 785 PHE cc_start: 0.8631 (p90) cc_final: 0.8423 (p90) REVERT: B 76 ASP cc_start: 0.8293 (t0) cc_final: 0.7970 (t0) REVERT: B 123 TYR cc_start: 0.8465 (m-10) cc_final: 0.8234 (m-80) REVERT: B 164 ILE cc_start: 0.9219 (mm) cc_final: 0.8963 (mp) REVERT: B 182 LYS cc_start: 0.9246 (tttm) cc_final: 0.8743 (tttt) REVERT: B 299 VAL cc_start: 0.8762 (t) cc_final: 0.8558 (t) REVERT: E 53 GLN cc_start: 0.8998 (mp10) cc_final: 0.8792 (mp10) REVERT: E 101 LEU cc_start: 0.9064 (tp) cc_final: 0.8828 (tt) REVERT: D 58 LEU cc_start: 0.8407 (mt) cc_final: 0.8109 (mt) REVERT: D 60 ASN cc_start: 0.8672 (m-40) cc_final: 0.8265 (m110) REVERT: D 89 GLN cc_start: 0.9177 (mt0) cc_final: 0.8542 (mm-40) REVERT: D 166 ARG cc_start: 0.8623 (mtt90) cc_final: 0.8395 (mtt90) REVERT: D 186 THR cc_start: 0.8772 (m) cc_final: 0.8572 (m) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.5103 time to fit residues: 182.5539 Evaluate side-chains 215 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 40 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 120 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 125 optimal weight: 0.0980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.136350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.103778 restraints weight = 73387.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.107236 restraints weight = 50596.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.107551 restraints weight = 38359.288| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10621 Z= 0.177 Angle : 0.499 4.301 14427 Z= 0.279 Chirality : 0.042 0.158 1564 Planarity : 0.004 0.040 1896 Dihedral : 4.946 88.935 1455 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.09 % Allowed : 0.81 % Favored : 99.10 % 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: 0.70 (0.23), residues: 1303 helix: 1.61 (0.31), residues: 291 sheet: 0.31 (0.24), residues: 413 loop : 0.14 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.004 0.001 HIS A 186 PHE 0.013 0.001 PHE A 188 TYR 0.015 0.001 TYR A 522 ARG 0.005 0.000 ARG D 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 1.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1293 ASN cc_start: 0.8898 (t0) cc_final: 0.8180 (p0) REVERT: A 232 ASP cc_start: 0.8822 (m-30) cc_final: 0.8447 (m-30) REVERT: A 371 GLN cc_start: 0.7573 (tp40) cc_final: 0.7027 (tp-100) REVERT: A 372 MET cc_start: 0.8178 (mpp) cc_final: 0.7526 (mpp) REVERT: A 648 PHE cc_start: 0.8521 (p90) cc_final: 0.8245 (p90) REVERT: B 76 ASP cc_start: 0.8251 (t0) cc_final: 0.7891 (t0) REVERT: B 123 TYR cc_start: 0.8554 (m-10) cc_final: 0.8230 (m-80) REVERT: B 157 VAL cc_start: 0.7838 (t) cc_final: 0.7595 (t) REVERT: B 164 ILE cc_start: 0.9266 (mm) cc_final: 0.8996 (mp) REVERT: E 53 GLN cc_start: 0.9010 (mp10) cc_final: 0.8798 (mp10) REVERT: E 101 LEU cc_start: 0.9059 (tp) cc_final: 0.8700 (tt) REVERT: D 58 LEU cc_start: 0.8414 (mt) cc_final: 0.8130 (mt) REVERT: D 60 ASN cc_start: 0.8671 (m-40) cc_final: 0.8278 (m110) REVERT: D 74 ASP cc_start: 0.8931 (m-30) cc_final: 0.8726 (m-30) REVERT: D 79 TYR cc_start: 0.9162 (m-80) cc_final: 0.8571 (m-10) REVERT: D 111 MET cc_start: 0.8162 (tpp) cc_final: 0.7925 (tpp) outliers start: 1 outliers final: 0 residues processed: 245 average time/residue: 0.5092 time to fit residues: 172.9511 Evaluate side-chains 200 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 71 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 33 optimal weight: 0.0010 chunk 106 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.132150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.093395 restraints weight = 74913.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095298 restraints weight = 40001.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096711 restraints weight = 25265.352| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 10621 Z= 0.432 Angle : 0.624 6.604 14427 Z= 0.358 Chirality : 0.043 0.163 1564 Planarity : 0.005 0.044 1896 Dihedral : 5.307 87.973 1455 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.09 % Allowed : 0.90 % Favored : 99.01 % 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: -0.02 (0.22), residues: 1303 helix: 0.62 (0.29), residues: 299 sheet: 0.08 (0.24), residues: 415 loop : -0.28 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 376 HIS 0.004 0.001 HIS A 533 PHE 0.022 0.002 PHE A 738 TYR 0.016 0.002 TYR D 184 ARG 0.006 0.001 ARG D 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1293 ASN cc_start: 0.8975 (t0) cc_final: 0.8228 (p0) REVERT: A 196 HIS cc_start: 0.8793 (m90) cc_final: 0.8567 (m90) REVERT: A 232 ASP cc_start: 0.8859 (m-30) cc_final: 0.8518 (m-30) REVERT: A 284 ILE cc_start: 0.7759 (mm) cc_final: 0.7059 (tp) REVERT: A 386 LYS cc_start: 0.9017 (tttp) cc_final: 0.8755 (ttmm) REVERT: A 539 MET cc_start: 0.9151 (tpp) cc_final: 0.8676 (tpp) REVERT: A 666 ASN cc_start: 0.7588 (m-40) cc_final: 0.7204 (p0) REVERT: B 76 ASP cc_start: 0.8206 (t0) cc_final: 0.7906 (t0) REVERT: B 123 TYR cc_start: 0.8668 (m-10) cc_final: 0.8111 (m-80) REVERT: E 53 GLN cc_start: 0.9075 (mp10) cc_final: 0.8861 (mp10) REVERT: D 58 LEU cc_start: 0.8513 (mt) cc_final: 0.8237 (mt) REVERT: D 60 ASN cc_start: 0.8799 (m-40) cc_final: 0.8408 (m110) REVERT: D 79 TYR cc_start: 0.9231 (m-80) cc_final: 0.8654 (m-10) REVERT: D 110 TYR cc_start: 0.8913 (t80) cc_final: 0.8664 (t80) outliers start: 1 outliers final: 1 residues processed: 227 average time/residue: 0.5532 time to fit residues: 172.6509 Evaluate side-chains 183 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 53 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN D 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.133722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.100968 restraints weight = 74056.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.104219 restraints weight = 53908.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104433 restraints weight = 42624.660| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10621 Z= 0.235 Angle : 0.523 4.611 14427 Z= 0.293 Chirality : 0.042 0.154 1564 Planarity : 0.004 0.047 1896 Dihedral : 5.081 85.050 1455 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.09 % Allowed : 0.90 % Favored : 99.01 % 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: 0.14 (0.22), residues: 1303 helix: 1.04 (0.29), residues: 284 sheet: 0.13 (0.24), residues: 420 loop : -0.28 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 546 HIS 0.003 0.001 HIS A 533 PHE 0.013 0.001 PHE E 77 TYR 0.017 0.001 TYR D 36 ARG 0.005 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2606 Ramachandran restraints generated. 1303 Oldfield, 0 Emsley, 1303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 1293 ASN cc_start: 0.8910 (t0) cc_final: 0.8203 (p0) REVERT: A 224 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8262 (mm-30) REVERT: A 284 ILE cc_start: 0.7843 (mm) cc_final: 0.6910 (tp) REVERT: A 539 MET cc_start: 0.9011 (tpp) cc_final: 0.8581 (tpp) REVERT: A 648 PHE cc_start: 0.8640 (p90) cc_final: 0.8336 (p90) REVERT: B 76 ASP cc_start: 0.8045 (t0) cc_final: 0.7709 (t0) REVERT: B 123 TYR cc_start: 0.8473 (m-10) cc_final: 0.8104 (m-80) REVERT: E 36 ASN cc_start: 0.8196 (m110) cc_final: 0.7370 (m-40) REVERT: E 53 GLN cc_start: 0.9055 (mp10) cc_final: 0.8837 (mp10) REVERT: D 58 LEU cc_start: 0.8454 (mt) cc_final: 0.8249 (mt) REVERT: D 60 ASN cc_start: 0.8713 (m-40) cc_final: 0.8327 (m110) REVERT: D 110 TYR cc_start: 0.8760 (t80) cc_final: 0.8501 (t80) outliers start: 1 outliers final: 0 residues processed: 228 average time/residue: 0.5462 time to fit residues: 172.3472 Evaluate side-chains 191 residues out of total 1107 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 54.7287 > 50: distance: 197 - 198: 3.148 distance: 197 - 205: 5.783 distance: 198 - 199: 5.219 distance: 198 - 201: 5.404 distance: 198 - 206: 6.741 distance: 199 - 200: 7.703 distance: 201 - 202: 5.535 distance: 201 - 207: 4.452 distance: 201 - 208: 7.286 distance: 202 - 203: 3.510 distance: 202 - 204: 5.251 distance: 202 - 209: 6.393 distance: 203 - 210: 4.453 distance: 203 - 211: 5.339 distance: 203 - 212: 7.184 distance: 204 - 214: 5.470 distance: 204 - 215: 3.372 distance: 217 - 218: 8.494 distance: 217 - 220: 7.533 distance: 217 - 222: 6.546 distance: 218 - 219: 7.165 distance: 218 - 226: 5.512 distance: 220 - 223: 6.517 distance: 220 - 224: 4.625 distance: 220 - 225: 9.692 distance: 226 - 227: 7.868 distance: 226 - 235: 13.041 distance: 227 - 228: 8.026 distance: 227 - 230: 7.317 distance: 227 - 236: 13.110 distance: 228 - 229: 9.776 distance: 228 - 241: 9.327 distance: 230 - 231: 12.109 distance: 230 - 237: 8.017 distance: 230 - 238: 4.335 distance: 231 - 232: 9.018 distance: 231 - 239: 7.901 distance: 231 - 240: 14.722 distance: 232 - 233: 5.704 distance: 232 - 234: 10.818 distance: 241 - 242: 7.233 distance: 241 - 249: 5.611 distance: 242 - 243: 10.019 distance: 242 - 250: 3.232 distance: 243 - 244: 4.882 distance: 243 - 260: 6.796 distance: 245 - 246: 10.059 distance: 245 - 251: 8.714 distance: 245 - 252: 8.739 distance: 246 - 247: 15.117 distance: 246 - 248: 9.223 distance: 246 - 253: 7.283 distance: 247 - 254: 7.520 distance: 247 - 255: 6.639 distance: 247 - 256: 5.429 distance: 248 - 257: 12.469 distance: 248 - 258: 9.770 distance: 248 - 259: 6.526 distance: 260 - 261: 9.275 distance: 260 - 270: 3.281 distance: 261 - 262: 10.088 distance: 261 - 264: 17.489 distance: 261 - 271: 3.537 distance: 262 - 263: 4.841 distance: 262 - 277: 10.798 distance: 264 - 265: 4.225 distance: 264 - 272: 3.943 distance: 264 - 273: 11.299 distance: 265 - 266: 18.722 distance: 265 - 267: 22.200 distance: 266 - 268: 10.657 distance: 267 - 269: 4.294 distance: 268 - 269: 27.720 distance: 268 - 275: 10.518 distance: 269 - 276: 4.437 distance: 277 - 278: 15.581 distance: 277 - 282: 21.000 distance: 278 - 279: 3.420 distance: 278 - 281: 8.153 distance: 278 - 283: 8.618 distance: 279 - 280: 6.138 distance: 279 - 287: 8.221 distance: 281 - 284: 6.470 distance: 281 - 285: 6.906 distance: 281 - 286: 7.117 distance: 287 - 288: 13.815 distance: 287 - 293: 12.411 distance: 288 - 291: 11.862 distance: 288 - 294: 4.709 distance: 289 - 301: 21.633 distance: 291 - 292: 11.708 distance: 292 - 293: 10.966 distance: 292 - 297: 4.912 distance: 292 - 298: 14.091 distance: 293 - 299: 10.503 distance: 293 - 300: 6.081 distance: 301 - 302: 28.035 distance: 301 - 306: 15.028 distance: 302 - 303: 17.800 distance: 302 - 305: 25.912 distance: 302 - 307: 8.490 distance: 303 - 304: 16.144 distance: 303 - 311: 31.629 distance: 305 - 308: 11.840 distance: 305 - 309: 5.137 distance: 305 - 310: 7.126 distance: 311 - 312: 7.717 distance: 311 - 315: 11.835 distance: 312 - 313: 13.957 distance: 312 - 316: 15.689 distance: 312 - 317: 16.366 distance: 313 - 314: 26.621 distance: 313 - 318: 6.725 distance: 318 - 319: 5.379 distance: 318 - 326: 9.577 distance: 319 - 320: 3.330 distance: 319 - 322: 5.683 distance: 319 - 327: 10.659 distance: 320 - 321: 8.335 distance: 320 - 335: 3.957 distance: 322 - 329: 4.783 distance: 323 - 324: 10.356 distance: 323 - 330: 10.487 distance: 323 - 331: 15.729 distance: 324 - 325: 7.898 distance: 325 - 333: 3.264 distance: 325 - 334: 3.093