Starting phenix.real_space_refine on Thu Jan 16 18:46:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bwp_16293/01_2025/8bwp_16293.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bwp_16293/01_2025/8bwp_16293.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bwp_16293/01_2025/8bwp_16293.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bwp_16293/01_2025/8bwp_16293.map" model { file = "/net/cci-nas-00/data/ceres_data/8bwp_16293/01_2025/8bwp_16293.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bwp_16293/01_2025/8bwp_16293.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 6221 2.51 5 N 1610 2.21 5 O 1704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 9578 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1195, 9545 Classifications: {'peptide': 1195} Link IDs: {'PTRANS': 37, 'TRANS': 1157} Chain breaks: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'MTX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.59, per 1000 atoms: 0.69 Number of scatterers: 9578 At special positions: 0 Unit cell: (77.376, 107.328, 144.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1704 8.00 N 1610 7.00 C 6221 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: 2.55 Conformation dependent library (CDL) restraints added in 1.1 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue is complicated and confusing pdb=" CB MTX A1401 " Number of C-beta restraints generated: 2266 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 5 sheets defined 73.1% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.742A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 75 removed outlier: 4.316A pdb=" N GLY A 62 " --> pdb=" O GLU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.769A pdb=" N ALA A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 85 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 121 removed outlier: 4.157A pdb=" N LEU A 93 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE A 101 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Proline residue: A 110 - end of helix removed outlier: 3.578A pdb=" N PHE A 120 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 150 Processing helix chain 'A' and resid 150 through 181 removed outlier: 3.956A pdb=" N LEU A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 166 " --> pdb=" O ALA A 162 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 201 through 203 No H-bonds generated for 'chain 'A' and resid 201 through 203' Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.337A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 212 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 235 through 246 removed outlier: 3.944A pdb=" N ALA A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 282 removed outlier: 3.893A pdb=" N LEU A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 291 through 342 removed outlier: 4.369A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ARG A 312 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 367 removed outlier: 3.690A pdb=" N ALA A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.509A pdb=" N LEU A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 513 through 521 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.534A pdb=" N LEU A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 551 " --> pdb=" O ARG A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 576 removed outlier: 4.392A pdb=" N PHE A 574 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 600 removed outlier: 3.873A pdb=" N LYS A 598 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 697 through 709 removed outlier: 3.505A pdb=" N GLY A 708 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 745 removed outlier: 3.647A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 808 removed outlier: 3.708A pdb=" N GLY A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.697A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.636A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE A 825 " --> pdb=" O ILE A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 835 removed outlier: 4.611A pdb=" N ASP A 833 " --> pdb=" O ILE A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 861 Processing helix chain 'A' and resid 864 through 896 Proline residue: A 870 - end of helix removed outlier: 3.599A pdb=" N ARG A 880 " --> pdb=" O ILE A 876 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.891A pdb=" N PHE A 901 " --> pdb=" O ARG A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.724A pdb=" N TYR A 917 " --> pdb=" O THR A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 970 removed outlier: 4.016A pdb=" N CYS A 923 " --> pdb=" O ALA A 919 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 927 " --> pdb=" O CYS A 923 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU A 933 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLU A 936 " --> pdb=" O ASP A 932 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 945 " --> pdb=" O PHE A 941 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 968 " --> pdb=" O ALA A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 987 Processing helix chain 'A' and resid 988 through 1007 removed outlier: 3.524A pdb=" N MET A 992 " --> pdb=" O THR A 988 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N TRP A 995 " --> pdb=" O GLY A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1018 removed outlier: 3.772A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A1018 " --> pdb=" O ILE A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 Processing helix chain 'A' and resid 1109 through 1116 removed outlier: 3.689A pdb=" N LYS A1115 " --> pdb=" O HIS A1111 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1161 Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1194 Processing helix chain 'A' and resid 1203 through 1207 Processing helix chain 'A' and resid 1208 through 1223 Processing helix chain 'A' and resid 1234 through 1238 Processing helix chain 'A' and resid 1257 through 1264 Processing helix chain 'A' and resid 1267 through 1275 Processing helix chain 'A' and resid 1276 through 1278 No H-bonds generated for 'chain 'A' and resid 1276 through 1278' Processing helix chain 'A' and resid 1279 through 1294 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435 removed outlier: 5.804A pdb=" N GLN A 429 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ALA A 417 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N PHE A 433 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLN A 413 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL A 435 " --> pdb=" O HIS A 411 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N HIS A 411 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE A 415 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N HIS A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.847A pdb=" N ALA A 476 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ALA A 442 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LEU A 606 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL A 444 " --> pdb=" O LEU A 606 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 487 through 488 removed outlier: 4.644A pdb=" N GLY A 487 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1058 through 1065 removed outlier: 5.790A pdb=" N LYS A1059 " --> pdb=" O PHE A1048 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE A1048 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ALA A1063 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP A1044 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE A1065 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE A1042 " --> pdb=" O ILE A1065 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A1046 " --> pdb=" O GLU A1095 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU A1095 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 6.451A pdb=" N LEU A1198 " --> pdb=" O LEU A1229 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE A1231 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A1200 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE A1244 " --> pdb=" O TYR A1255 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TYR A1255 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL A1246 " --> pdb=" O LYS A1253 " (cutoff:3.500A) 609 hydrogen bonds defined for protein. 1761 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.88 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: 1.22 - 1.34: 3024 1.34 - 1.46: 1607 1.46 - 1.58: 5082 1.58 - 1.69: 1 1.69 - 1.81: 70 Bond restraints: 9784 Sorted by residual: bond pdb=" C2 MTX A1401 " pdb=" NA2 MTX A1401 " ideal model delta sigma weight residual 1.341 1.407 -0.066 2.00e-02 2.50e+03 1.08e+01 bond pdb=" CG LEU A 27 " pdb=" CD1 LEU A 27 " ideal model delta sigma weight residual 1.521 1.440 0.081 3.30e-02 9.18e+02 5.97e+00 bond pdb=" CB GLN A 931 " pdb=" CG GLN A 931 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.12e+00 bond pdb=" C8A MTX A1401 " pdb=" N8 MTX A1401 " ideal model delta sigma weight residual 1.348 1.393 -0.045 2.00e-02 2.50e+03 5.09e+00 bond pdb=" CB ARG A 946 " pdb=" CG ARG A 946 " ideal model delta sigma weight residual 1.520 1.452 0.068 3.00e-02 1.11e+03 5.09e+00 ... (remaining 9779 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 12676 1.88 - 3.77: 488 3.77 - 5.65: 75 5.65 - 7.54: 18 7.54 - 9.42: 5 Bond angle restraints: 13262 Sorted by residual: angle pdb=" C THR A 943 " pdb=" N THR A 944 " pdb=" CA THR A 944 " ideal model delta sigma weight residual 120.29 115.76 4.53 1.42e+00 4.96e-01 1.02e+01 angle pdb=" CB ARG A 951 " pdb=" CG ARG A 951 " pdb=" CD ARG A 951 " ideal model delta sigma weight residual 111.30 118.25 -6.95 2.30e+00 1.89e-01 9.12e+00 angle pdb=" CA GLN A 849 " pdb=" CB GLN A 849 " pdb=" CG GLN A 849 " ideal model delta sigma weight residual 114.10 120.10 -6.00 2.00e+00 2.50e-01 9.00e+00 angle pdb=" C HIS A 153 " pdb=" N LEU A 154 " pdb=" CA LEU A 154 " ideal model delta sigma weight residual 120.29 116.07 4.22 1.42e+00 4.96e-01 8.84e+00 angle pdb=" CA ARG A 951 " pdb=" CB ARG A 951 " pdb=" CG ARG A 951 " ideal model delta sigma weight residual 114.10 119.50 -5.40 2.00e+00 2.50e-01 7.30e+00 ... (remaining 13257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 5411 16.96 - 33.92: 329 33.92 - 50.87: 71 50.87 - 67.83: 17 67.83 - 84.79: 7 Dihedral angle restraints: 5835 sinusoidal: 2341 harmonic: 3494 Sorted by residual: dihedral pdb=" CA LEU A1091 " pdb=" C LEU A1091 " pdb=" N SER A1092 " pdb=" CA SER A1092 " ideal model delta harmonic sigma weight residual 180.00 154.13 25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA CYS A1226 " pdb=" C CYS A1226 " pdb=" N THR A1227 " pdb=" CA THR A1227 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA LYS A1021 " pdb=" C LYS A1021 " pdb=" N GLU A1022 " pdb=" CA GLU A1022 " ideal model delta harmonic sigma weight residual 180.00 156.39 23.61 0 5.00e+00 4.00e-02 2.23e+01 ... (remaining 5832 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1187 0.068 - 0.136: 309 0.136 - 0.204: 38 0.204 - 0.272: 3 0.272 - 0.340: 1 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA MTX A1401 " pdb=" N MTX A1401 " pdb=" CB MTX A1401 " pdb=" CT MTX A1401 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA PHE A 258 " pdb=" N PHE A 258 " pdb=" C PHE A 258 " pdb=" CB PHE A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA PHE A 24 " pdb=" N PHE A 24 " pdb=" C PHE A 24 " pdb=" CB PHE A 24 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1535 not shown) Planarity restraints: 1646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 26 " -0.020 2.00e-02 2.50e+03 1.55e-02 5.98e+00 pdb=" CG TRP A 26 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 26 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 26 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 26 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 26 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 26 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 26 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 26 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 26 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 939 " -0.024 2.00e-02 2.50e+03 1.84e-02 5.91e+00 pdb=" CG PHE A 939 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 939 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 939 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 939 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 939 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 939 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1292 " 0.009 2.00e-02 2.50e+03 1.64e-02 5.40e+00 pdb=" CG TYR A1292 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A1292 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR A1292 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A1292 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR A1292 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1292 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR A1292 " 0.027 2.00e-02 2.50e+03 ... (remaining 1643 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1421 2.75 - 3.29: 10324 3.29 - 3.83: 15536 3.83 - 4.36: 18837 4.36 - 4.90: 31944 Nonbonded interactions: 78062 Sorted by model distance: nonbonded pdb=" NH1 ARG A 303 " pdb=" OE1 GLU A 306 " model vdw 2.213 3.120 nonbonded pdb=" OH TYR A 92 " pdb=" O THR A 209 " model vdw 2.214 3.040 nonbonded pdb=" O SER A1241 " pdb=" OH TYR A1292 " model vdw 2.219 3.040 nonbonded pdb=" O GLU A 521 " pdb=" OG1 THR A 526 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR A 269 " pdb=" OE2 GLU A 306 " model vdw 2.247 3.040 ... (remaining 78057 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.280 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.011 0.081 9784 Z= 0.704 Angle : 0.899 9.422 13262 Z= 0.492 Chirality : 0.060 0.340 1538 Planarity : 0.008 0.078 1646 Dihedral : 12.537 84.791 3569 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.48 % Allowed : 1.82 % Favored : 97.70 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1187 helix: -1.44 (0.15), residues: 769 sheet: 0.56 (0.78), residues: 50 loop : 0.32 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A 26 HIS 0.014 0.002 HIS A 172 PHE 0.042 0.004 PHE A 939 TYR 0.028 0.005 TYR A 881 ARG 0.023 0.003 ARG A 897 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 207 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8467 (t0) cc_final: 0.8211 (t0) REVERT: A 67 GLU cc_start: 0.8510 (tp30) cc_final: 0.8278 (tp30) REVERT: A 200 ASN cc_start: 0.8411 (t0) cc_final: 0.7787 (t0) REVERT: A 206 ASP cc_start: 0.7918 (t70) cc_final: 0.7708 (t70) REVERT: A 276 MET cc_start: 0.8329 (tpp) cc_final: 0.8109 (tpp) REVERT: A 316 LEU cc_start: 0.8398 (tp) cc_final: 0.7992 (tt) REVERT: A 728 TYR cc_start: 0.8546 (t80) cc_final: 0.8310 (t80) REVERT: A 953 ASP cc_start: 0.8492 (m-30) cc_final: 0.7945 (m-30) REVERT: A 985 TYR cc_start: 0.8166 (m-80) cc_final: 0.7717 (m-80) REVERT: A 998 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.7020 (mmt-90) REVERT: A 1045 ASN cc_start: 0.9065 (t0) cc_final: 0.8806 (t0) REVERT: A 1104 LEU cc_start: 0.9073 (tp) cc_final: 0.8539 (tp) REVERT: A 1122 GLN cc_start: 0.7517 (tt0) cc_final: 0.6847 (tm-30) REVERT: A 1136 ASP cc_start: 0.7587 (t0) cc_final: 0.6875 (t0) REVERT: A 1196 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7621 (mp10) REVERT: A 1212 ASP cc_start: 0.8769 (t0) cc_final: 0.8278 (m-30) REVERT: A 1253 LYS cc_start: 0.9069 (mmtt) cc_final: 0.8766 (mmtm) outliers start: 5 outliers final: 3 residues processed: 211 average time/residue: 0.2780 time to fit residues: 77.7037 Evaluate side-chains 140 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 137 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 944 THR Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 0.0870 chunk 36 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 994 GLN ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.200206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.158810 restraints weight = 11455.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156921 restraints weight = 13225.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.158065 restraints weight = 13191.782| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9784 Z= 0.260 Angle : 0.612 7.709 13262 Z= 0.331 Chirality : 0.043 0.173 1538 Planarity : 0.004 0.039 1646 Dihedral : 6.777 82.668 1304 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.82 % Allowed : 8.06 % Favored : 90.12 % Cbeta Deviations : 0.09 % 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: 0.38 (0.24), residues: 1187 helix: 0.26 (0.18), residues: 788 sheet: 0.55 (0.76), residues: 52 loop : 0.61 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 711 HIS 0.006 0.001 HIS A1225 PHE 0.033 0.002 PHE A 258 TYR 0.023 0.002 TYR A1292 ARG 0.009 0.001 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 ASN cc_start: 0.8409 (t0) cc_final: 0.8176 (t0) REVERT: A 706 ARG cc_start: 0.7916 (tpp-160) cc_final: 0.7576 (mmt180) REVERT: A 744 MET cc_start: 0.7385 (mmm) cc_final: 0.6859 (mtp) REVERT: A 1016 TYR cc_start: 0.7768 (m-10) cc_final: 0.6662 (m-10) REVERT: A 1136 ASP cc_start: 0.7800 (t0) cc_final: 0.7172 (t70) outliers start: 19 outliers final: 15 residues processed: 194 average time/residue: 0.2196 time to fit residues: 60.3560 Evaluate side-chains 155 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 183 ASN Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 388 THR Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1230 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 45 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1134 ASN A1206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.199805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158883 restraints weight = 11619.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.158590 restraints weight = 14736.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159437 restraints weight = 13382.823| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9784 Z= 0.241 Angle : 0.582 7.290 13262 Z= 0.309 Chirality : 0.043 0.175 1538 Planarity : 0.004 0.035 1646 Dihedral : 6.494 86.890 1303 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.17 % Allowed : 11.23 % Favored : 85.60 % Cbeta Deviations : 0.09 % 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: 0.80 (0.25), residues: 1187 helix: 0.60 (0.18), residues: 786 sheet: 1.25 (0.83), residues: 47 loop : 0.63 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 89 HIS 0.004 0.001 HIS A 934 PHE 0.033 0.002 PHE A 258 TYR 0.021 0.002 TYR A 289 ARG 0.005 0.000 ARG A1030 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLN cc_start: 0.8651 (tp40) cc_final: 0.8318 (tp40) REVERT: A 67 GLU cc_start: 0.8707 (tp30) cc_final: 0.8391 (tp30) REVERT: A 706 ARG cc_start: 0.7942 (tpp-160) cc_final: 0.7551 (mmt180) REVERT: A 744 MET cc_start: 0.7482 (mmm) cc_final: 0.6873 (mtp) REVERT: A 904 LEU cc_start: 0.8372 (tp) cc_final: 0.8161 (tp) REVERT: A 1016 TYR cc_start: 0.7619 (m-10) cc_final: 0.6668 (m-10) REVERT: A 1122 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7738 (tp40) REVERT: A 1136 ASP cc_start: 0.7918 (t0) cc_final: 0.7223 (t0) outliers start: 33 outliers final: 24 residues processed: 180 average time/residue: 0.2196 time to fit residues: 56.1375 Evaluate side-chains 157 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 TRP Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 PHE Chi-restraints excluded: chain A residue 710 HIS Chi-restraints excluded: chain A residue 765 LEU Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 902 SER Chi-restraints excluded: chain A residue 956 CYS Chi-restraints excluded: chain A residue 1005 ASN Chi-restraints excluded: chain A residue 1049 MET Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1064 LEU Chi-restraints excluded: chain A residue 1082 SER 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: 58.195 > 50: distance: 48 - 73: 12.836 distance: 53 - 57: 17.018 distance: 54 - 79: 3.171 distance: 57 - 58: 15.553 distance: 58 - 59: 8.664 distance: 58 - 61: 5.668 distance: 59 - 60: 14.639 distance: 59 - 65: 4.053 distance: 60 - 84: 19.490 distance: 61 - 62: 10.452 distance: 62 - 63: 6.158 distance: 62 - 64: 7.913 distance: 65 - 66: 5.833 distance: 66 - 67: 6.913 distance: 66 - 69: 7.383 distance: 67 - 73: 7.559 distance: 68 - 91: 7.245 distance: 69 - 70: 7.729 distance: 70 - 71: 7.492 distance: 70 - 72: 6.643 distance: 73 - 74: 5.692 distance: 74 - 75: 4.955 distance: 74 - 77: 11.111 distance: 75 - 76: 15.180 distance: 75 - 79: 3.839 distance: 76 - 99: 19.748 distance: 77 - 78: 7.066 distance: 79 - 80: 4.122 distance: 80 - 81: 3.516 distance: 81 - 84: 7.516 distance: 84 - 85: 8.717 distance: 85 - 86: 10.280 distance: 85 - 88: 3.448 distance: 86 - 87: 16.242 distance: 86 - 91: 3.730 distance: 88 - 89: 5.900 distance: 88 - 90: 9.867 distance: 91 - 92: 11.520 distance: 92 - 93: 8.385 distance: 92 - 95: 8.956 distance: 93 - 94: 9.640 distance: 93 - 99: 9.900 distance: 95 - 96: 14.544 distance: 96 - 97: 3.655 distance: 96 - 98: 7.269 distance: 99 - 100: 11.839 distance: 100 - 101: 3.266 distance: 101 - 102: 11.920 distance: 103 - 104: 3.002 distance: 104 - 105: 5.341 distance: 104 - 107: 4.909 distance: 105 - 106: 15.561 distance: 105 - 112: 4.080 distance: 107 - 108: 5.195 distance: 108 - 109: 6.564 distance: 109 - 110: 4.000 distance: 109 - 111: 3.775 distance: 112 - 113: 8.820 distance: 113 - 114: 21.146 distance: 113 - 116: 7.776 distance: 114 - 115: 38.535 distance: 114 - 120: 58.195 distance: 116 - 117: 3.034 distance: 117 - 118: 7.939 distance: 117 - 119: 12.242 distance: 120 - 121: 49.516 distance: 121 - 122: 20.443 distance: 121 - 124: 44.475 distance: 122 - 123: 17.974 distance: 122 - 125: 9.581