Starting phenix.real_space_refine on Fri May 16 21:06:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7d_41979/05_2025/8u7d_41979.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7d_41979/05_2025/8u7d_41979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7d_41979/05_2025/8u7d_41979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7d_41979/05_2025/8u7d_41979.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7d_41979/05_2025/8u7d_41979.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7d_41979/05_2025/8u7d_41979.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.016 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 P 3 5.49 5 S 76 5.16 5 C 9757 2.51 5 N 2412 2.21 5 O 2676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14924 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 923, 7267 Classifications: {'peptide': 923} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 893} Chain breaks: 4 Chain: "B" Number of atoms: 7267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 923, 7267 Classifications: {'peptide': 923} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 893} Chain breaks: 4 Chain: "A" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 281 Unusual residues: {'AJP': 3, 'POV': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 27 Chain: "B" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'AJP': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 9.42, per 1000 atoms: 0.63 Number of scatterers: 14924 At special positions: 0 Unit cell: (112.2, 133.96, 125.12, 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 76 16.00 P 3 15.00 O 2676 8.00 N 2412 7.00 C 9757 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: 4.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 9 sheets defined 74.7% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 102 through 120 removed outlier: 3.525A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.700A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 141 removed outlier: 3.861A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 154 removed outlier: 3.614A pdb=" N VAL A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.675A pdb=" N SER A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 189 removed outlier: 4.054A pdb=" N ILE A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 209 through 221 removed outlier: 4.291A pdb=" N VAL A 213 " --> pdb=" O ASP A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 254 removed outlier: 3.691A pdb=" N PHE A 254 " --> pdb=" O LYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 291 removed outlier: 4.292A pdb=" N GLY A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 296 through 317 removed outlier: 3.816A pdb=" N GLU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 322 Processing helix chain 'A' and resid 323 through 337 removed outlier: 3.940A pdb=" N VAL A 327 " --> pdb=" O GLY A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 375 Processing helix chain 'A' and resid 381 through 414 removed outlier: 3.617A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR A 396 " --> pdb=" O TYR A 392 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 428 Processing helix chain 'A' and resid 432 through 447 removed outlier: 3.988A pdb=" N LEU A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 482 removed outlier: 4.403A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 513 Processing helix chain 'A' and resid 522 through 529 removed outlier: 3.958A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 600 Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 627 through 632 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 640 through 652 removed outlier: 3.670A pdb=" N LEU A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 771 Processing helix chain 'A' and resid 807 through 810 removed outlier: 3.717A pdb=" N MET A 810 " --> pdb=" O GLY A 807 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 807 through 810' Processing helix chain 'A' and resid 811 through 851 removed outlier: 4.100A pdb=" N LYS A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 3.833A pdb=" N ILE A 822 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LEU A 835 " --> pdb=" O ASN A 831 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY A 842 " --> pdb=" O ASP A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 858 Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.588A pdb=" N LEU A 864 " --> pdb=" O ASN A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 919 removed outlier: 3.546A pdb=" N ALA A 893 " --> pdb=" O HIS A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 942 Processing helix chain 'A' and resid 952 through 959 Processing helix chain 'A' and resid 966 through 976 removed outlier: 3.695A pdb=" N ILE A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1050 Processing helix chain 'A' and resid 1070 through 1080 Processing helix chain 'A' and resid 1085 through 1107 Proline residue: A1101 - end of helix Processing helix chain 'A' and resid 1113 through 1124 removed outlier: 3.552A pdb=" N GLY A1124 " --> pdb=" O HIS A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1158 Processing helix chain 'B' and resid 77 through 95 Processing helix chain 'B' and resid 102 through 120 removed outlier: 3.536A pdb=" N LEU B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 4.705A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 141 removed outlier: 3.870A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 154 removed outlier: 3.552A pdb=" N VAL B 145 " --> pdb=" O ILE B 141 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B 154 " --> pdb=" O SER B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 removed outlier: 3.521A pdb=" N ARG B 161 " --> pdb=" O HIS B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 189 removed outlier: 3.805A pdb=" N PHE B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 205 removed outlier: 3.836A pdb=" N PHE B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 4.410A pdb=" N VAL B 213 " --> pdb=" O ASP B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 254 removed outlier: 3.665A pdb=" N PHE B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 291 removed outlier: 4.285A pdb=" N GLY B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 296 through 317 removed outlier: 3.801A pdb=" N GLU B 300 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 322 Processing helix chain 'B' and resid 323 through 337 removed outlier: 3.937A pdb=" N VAL B 327 " --> pdb=" O GLY B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 375 Processing helix chain 'B' and resid 381 through 414 removed outlier: 3.623A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR B 396 " --> pdb=" O TYR B 392 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 428 Processing helix chain 'B' and resid 432 through 447 removed outlier: 3.970A pdb=" N LEU B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 482 removed outlier: 4.398A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 513 Processing helix chain 'B' and resid 522 through 529 removed outlier: 3.977A pdb=" N ALA B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 600 Processing helix chain 'B' and resid 604 through 621 Processing helix chain 'B' and resid 627 through 632 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 640 through 652 removed outlier: 3.662A pdb=" N LEU B 644 " --> pdb=" O ILE B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 771 Processing helix chain 'B' and resid 807 through 810 removed outlier: 3.833A pdb=" N MET B 810 " --> pdb=" O GLY B 807 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 807 through 810' Processing helix chain 'B' and resid 811 through 817 removed outlier: 4.114A pdb=" N LYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 816 " --> pdb=" O ARG B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 856 removed outlier: 3.719A pdb=" N LEU B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU B 835 " --> pdb=" O ASN B 831 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 836 " --> pdb=" O GLN B 832 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY B 842 " --> pdb=" O ASP B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.520A pdb=" N LEU B 864 " --> pdb=" O ASN B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 919 removed outlier: 3.557A pdb=" N ALA B 893 " --> pdb=" O HIS B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 942 Processing helix chain 'B' and resid 952 through 959 Processing helix chain 'B' and resid 966 through 976 removed outlier: 3.694A pdb=" N ILE B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 1043 through 1050 Processing helix chain 'B' and resid 1070 through 1080 Processing helix chain 'B' and resid 1085 through 1107 Proline residue: B1101 - end of helix Processing helix chain 'B' and resid 1113 through 1124 removed outlier: 3.541A pdb=" N GLY B1124 " --> pdb=" O HIS B1120 " (cutoff:3.500A) Processing helix chain 'B' and resid 1155 through 1158 Processing sheet with id=AA1, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.730A pdb=" N GLN A1064 " --> pdb=" O VAL A1002 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1032 through 1036 Processing sheet with id=AA3, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 4.204A pdb=" N LEU A1186 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1136 removed outlier: 3.623A pdb=" N LEU A1174 " --> pdb=" O PHE A1136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 978 through 982 Processing sheet with id=AA6, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.662A pdb=" N TYR B1066 " --> pdb=" O ILE B1001 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N ILE B1001 " --> pdb=" O TYR B1066 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1032 through 1036 Processing sheet with id=AA8, first strand: chain 'B' and resid 1125 through 1127 removed outlier: 4.178A pdb=" N LEU B1186 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE B1187 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU B1147 " --> pdb=" O PHE B1187 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL B1189 " --> pdb=" O VAL B1145 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N VAL B1145 " --> pdb=" O VAL B1189 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1135 through 1136 removed outlier: 3.642A pdb=" N LEU B1174 " --> pdb=" O PHE B1136 " (cutoff:3.500A) 1048 hydrogen bonds defined for protein. 3084 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: 5.23 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2432 1.32 - 1.44: 3799 1.44 - 1.57: 8862 1.57 - 1.69: 6 1.69 - 1.81: 140 Bond restraints: 15239 Sorted by residual: bond pdb=" C ILE A 488 " pdb=" N PRO A 489 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.38e-02 5.25e+03 2.86e+00 bond pdb=" C26 AJP B1402 " pdb=" O25 AJP B1402 " ideal model delta sigma weight residual 1.375 1.406 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C26 AJP A1404 " pdb=" O25 AJP A1404 " ideal model delta sigma weight residual 1.375 1.406 -0.031 2.00e-02 2.50e+03 2.34e+00 bond pdb=" C35 AJP A1404 " pdb=" O34 AJP A1404 " ideal model delta sigma weight residual 1.380 1.409 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C26 AJP A1405 " pdb=" O25 AJP A1405 " ideal model delta sigma weight residual 1.375 1.404 -0.029 2.00e-02 2.50e+03 2.12e+00 ... (remaining 15234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 20262 1.89 - 3.77: 368 3.77 - 5.66: 65 5.66 - 7.55: 12 7.55 - 9.44: 3 Bond angle restraints: 20710 Sorted by residual: angle pdb=" C37 AJP A1405 " pdb=" C36 AJP A1405 " pdb=" O54 AJP A1405 " ideal model delta sigma weight residual 105.10 114.47 -9.37 3.00e+00 1.11e-01 9.76e+00 angle pdb=" CA LEU B 174 " pdb=" CB LEU B 174 " pdb=" CG LEU B 174 " ideal model delta sigma weight residual 116.30 106.86 9.44 3.50e+00 8.16e-02 7.27e+00 angle pdb=" C HIS B1156 " pdb=" N THR B1157 " pdb=" CA THR B1157 " ideal model delta sigma weight residual 121.54 126.34 -4.80 1.91e+00 2.74e-01 6.31e+00 angle pdb=" C HIS A1156 " pdb=" N THR A1157 " pdb=" CA THR A1157 " ideal model delta sigma weight residual 121.54 126.32 -4.78 1.91e+00 2.74e-01 6.26e+00 angle pdb=" C35 AJP A1405 " pdb=" C36 AJP A1405 " pdb=" O54 AJP A1405 " ideal model delta sigma weight residual 112.23 104.88 7.35 3.00e+00 1.11e-01 6.00e+00 ... (remaining 20705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.78: 8787 23.78 - 47.56: 695 47.56 - 71.34: 117 71.34 - 95.12: 24 95.12 - 118.90: 20 Dihedral angle restraints: 9643 sinusoidal: 4291 harmonic: 5352 Sorted by residual: dihedral pdb=" C29 AJP B1402 " pdb=" C30 AJP B1402 " pdb=" C32 AJP B1402 " pdb=" O33 AJP B1402 " ideal model delta sinusoidal sigma weight residual -60.96 -179.86 118.90 1 3.00e+01 1.11e-03 1.58e+01 dihedral pdb=" O31 AJP B1402 " pdb=" C30 AJP B1402 " pdb=" C32 AJP B1402 " pdb=" O33 AJP B1402 " ideal model delta sinusoidal sigma weight residual 177.28 59.18 118.10 1 3.00e+01 1.11e-03 1.57e+01 dihedral pdb=" C56 AJP B1402 " pdb=" C57 AJP B1402 " pdb=" C58 AJP B1402 " pdb=" C59 AJP B1402 " ideal model delta sinusoidal sigma weight residual 57.61 -59.20 116.81 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 9640 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2214 0.063 - 0.125: 283 0.125 - 0.188: 19 0.188 - 0.250: 8 0.250 - 0.313: 1 Chirality restraints: 2525 Sorted by residual: chirality pdb=" CG LEU B 174 " pdb=" CB LEU B 174 " pdb=" CD1 LEU B 174 " pdb=" CD2 LEU B 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.28 -0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" C55 AJP A1405 " pdb=" C56 AJP A1405 " pdb=" O54 AJP A1405 " pdb=" O60 AJP A1405 " both_signs ideal model delta sigma weight residual False 2.13 2.37 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C10 AJP B1402 " pdb=" C08 AJP B1402 " pdb=" C11 AJP B1402 " pdb=" O82 AJP B1402 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2522 not shown) Planarity restraints: 2493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO B 642 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 641 " 0.049 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO A 642 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 195 " -0.018 2.00e-02 2.50e+03 1.69e-02 5.01e+00 pdb=" CG PHE B 195 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE B 195 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE B 195 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 195 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 195 " -0.012 2.00e-02 2.50e+03 pdb=" CZ PHE B 195 " 0.000 2.00e-02 2.50e+03 ... (remaining 2490 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4379 2.83 - 3.34: 14505 3.34 - 3.86: 23881 3.86 - 4.38: 25448 4.38 - 4.90: 45968 Nonbonded interactions: 114181 Sorted by model distance: nonbonded pdb=" O MET A 154 " pdb=" ND2 ASN A 335 " model vdw 2.308 3.120 nonbonded pdb=" NE2 GLN A 225 " pdb=" OE1 GLN A 613 " model vdw 2.317 3.120 nonbonded pdb=" O GLY A1150 " pdb=" OG SER A1163 " model vdw 2.322 3.040 nonbonded pdb=" N ASP A 520 " pdb=" OD1 ASP A 520 " model vdw 2.323 3.120 nonbonded pdb=" OH TYR B 191 " pdb=" OD1 ASP B 384 " model vdw 2.334 3.040 ... (remaining 114176 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 74 through 1192 or resid 1401)) selection = (chain 'B' and (resid 74 through 1192 or resid 1401)) } 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: 8.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 35.040 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 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 0.040 15239 Z= 0.185 Angle : 0.633 9.436 20710 Z= 0.315 Chirality : 0.044 0.313 2525 Planarity : 0.005 0.074 2493 Dihedral : 17.899 118.903 6175 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.00 % Allowed : 23.26 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 0.76 (0.19), residues: 1826 helix: 1.04 (0.14), residues: 1320 sheet: -0.28 (0.48), residues: 116 loop : -0.84 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 643 HIS 0.005 0.001 HIS A 928 PHE 0.037 0.001 PHE B 195 TYR 0.019 0.001 TYR A 309 ARG 0.002 0.000 ARG B 431 Details of bonding type rmsd hydrogen bonds : bond 0.12340 ( 1042) hydrogen bonds : angle 5.42029 ( 3084) covalent geometry : bond 0.00408 (15239) covalent geometry : angle 0.63298 (20710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.576 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: A 160 MET cc_start: 0.7295 (ttt) cc_final: 0.6960 (ttp) REVERT: A 199 MET cc_start: 0.8473 (mmm) cc_final: 0.8081 (tpp) REVERT: A 959 ASN cc_start: 0.8412 (t0) cc_final: 0.8134 (t0) REVERT: A 1173 LYS cc_start: 0.3430 (pttm) cc_final: 0.3146 (mttp) REVERT: A 1185 ARG cc_start: 0.7141 (mtm-85) cc_final: 0.6393 (ttp80) REVERT: B 1098 ILE cc_start: 0.8895 (tp) cc_final: 0.8569 (tp) REVERT: B 1173 LYS cc_start: 0.5565 (mptt) cc_final: 0.4990 (mptt) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.2746 time to fit residues: 105.4050 Evaluate side-chains 207 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 155 optimal weight: 3.9990 chunk 139 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A 614 HIS A 832 GLN A 981 HIS ** A1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.191524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.132544 restraints weight = 18359.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130878 restraints weight = 25229.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132557 restraints weight = 18719.613| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 15239 Z= 0.251 Angle : 0.671 9.920 20710 Z= 0.331 Chirality : 0.042 0.297 2525 Planarity : 0.005 0.067 2493 Dihedral : 9.908 83.670 2767 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 5.01 % Allowed : 22.37 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.29 (0.19), residues: 1826 helix: 1.53 (0.14), residues: 1310 sheet: -0.22 (0.48), residues: 116 loop : -0.96 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 643 HIS 0.009 0.002 HIS A 928 PHE 0.019 0.002 PHE B1032 TYR 0.021 0.002 TYR B 309 ARG 0.007 0.000 ARG B1089 Details of bonding type rmsd hydrogen bonds : bond 0.05733 ( 1042) hydrogen bonds : angle 4.16188 ( 3084) covalent geometry : bond 0.00624 (15239) covalent geometry : angle 0.67055 (20710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 215 time to evaluate : 1.567 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: A 199 MET cc_start: 0.8564 (mmm) cc_final: 0.8217 (tpp) REVERT: A 611 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8694 (mm) REVERT: A 817 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8673 (tp) REVERT: A 959 ASN cc_start: 0.8526 (t0) cc_final: 0.8196 (t0) REVERT: A 1173 LYS cc_start: 0.3407 (pttm) cc_final: 0.3113 (mttp) REVERT: B 172 PHE cc_start: 0.7556 (OUTLIER) cc_final: 0.7193 (m-80) REVERT: B 611 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8634 (mm) REVERT: B 1098 ILE cc_start: 0.8669 (tp) cc_final: 0.8373 (tp) REVERT: B 1173 LYS cc_start: 0.5385 (mptt) cc_final: 0.4699 (mptt) outliers start: 79 outliers final: 52 residues processed: 271 average time/residue: 0.2174 time to fit residues: 91.6068 Evaluate side-chains 257 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 201 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 898 THR Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 995 SER Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 94 LEU Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 814 THR Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 898 THR Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1096 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 129 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 180 optimal weight: 40.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.195502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.140792 restraints weight = 18311.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.131011 restraints weight = 21608.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.129951 restraints weight = 15160.567| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15239 Z= 0.125 Angle : 0.541 8.521 20710 Z= 0.269 Chirality : 0.038 0.274 2525 Planarity : 0.004 0.065 2493 Dihedral : 7.718 69.000 2767 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.12 % Allowed : 23.95 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.78 (0.20), residues: 1826 helix: 1.95 (0.14), residues: 1310 sheet: -0.16 (0.49), residues: 116 loop : -0.99 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 643 HIS 0.009 0.001 HIS B 928 PHE 0.025 0.001 PHE B 972 TYR 0.017 0.001 TYR B1125 ARG 0.005 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 1042) hydrogen bonds : angle 3.81392 ( 3084) covalent geometry : bond 0.00275 (15239) covalent geometry : angle 0.54060 (20710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 223 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 611 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8707 (mm) REVERT: A 868 LYS cc_start: 0.8976 (mmtm) cc_final: 0.8701 (mmmm) REVERT: A 959 ASN cc_start: 0.8649 (t0) cc_final: 0.8228 (t0) REVERT: A 1044 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: A 1173 LYS cc_start: 0.3507 (pttm) cc_final: 0.3192 (mttp) REVERT: B 154 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.7362 (ppp) REVERT: B 611 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8665 (mm) REVERT: B 1072 ASP cc_start: 0.7485 (m-30) cc_final: 0.7241 (m-30) REVERT: B 1173 LYS cc_start: 0.5729 (mptt) cc_final: 0.5015 (mptt) outliers start: 65 outliers final: 32 residues processed: 262 average time/residue: 0.2342 time to fit residues: 95.7255 Evaluate side-chains 237 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 201 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 424 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1045 MET Chi-restraints excluded: chain B residue 1174 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 74 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 157 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.195369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.138289 restraints weight = 18434.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.131605 restraints weight = 23089.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.127873 restraints weight = 14463.356| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15239 Z= 0.127 Angle : 0.537 9.313 20710 Z= 0.266 Chirality : 0.038 0.224 2525 Planarity : 0.004 0.063 2493 Dihedral : 7.333 68.695 2767 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.82 % Allowed : 23.38 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.98 (0.20), residues: 1826 helix: 2.10 (0.14), residues: 1308 sheet: -0.03 (0.50), residues: 108 loop : -0.90 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 643 HIS 0.008 0.001 HIS B 928 PHE 0.024 0.001 PHE B1032 TYR 0.018 0.001 TYR A 309 ARG 0.004 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 1042) hydrogen bonds : angle 3.68359 ( 3084) covalent geometry : bond 0.00288 (15239) covalent geometry : angle 0.53676 (20710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 215 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.8561 (mmm) cc_final: 0.8183 (tpp) REVERT: A 444 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7062 (m110) REVERT: A 483 MET cc_start: 0.8406 (mmp) cc_final: 0.7834 (mmt) REVERT: A 611 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8726 (mm) REVERT: A 1173 LYS cc_start: 0.3409 (pttm) cc_final: 0.3094 (mttp) REVERT: B 154 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7350 (ppp) REVERT: B 172 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: B 420 ARG cc_start: 0.7566 (ptp90) cc_final: 0.7305 (ptp90) REVERT: B 477 LEU cc_start: 0.8853 (tp) cc_final: 0.8509 (tt) REVERT: B 611 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8684 (mm) REVERT: B 1072 ASP cc_start: 0.7648 (m-30) cc_final: 0.7326 (m-30) REVERT: B 1173 LYS cc_start: 0.5640 (mptt) cc_final: 0.4819 (mptt) outliers start: 76 outliers final: 43 residues processed: 263 average time/residue: 0.2102 time to fit residues: 87.3716 Evaluate side-chains 253 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 205 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 814 THR Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1174 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 43 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 157 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 141 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 181 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 0.4980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1040 ASN B 981 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.195245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.139543 restraints weight = 19035.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.139733 restraints weight = 30404.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140152 restraints weight = 21361.260| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15239 Z= 0.140 Angle : 0.548 9.119 20710 Z= 0.271 Chirality : 0.038 0.242 2525 Planarity : 0.004 0.063 2493 Dihedral : 7.250 68.426 2767 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.82 % Allowed : 23.83 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.20), residues: 1826 helix: 2.10 (0.14), residues: 1310 sheet: -0.01 (0.51), residues: 108 loop : -0.86 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 962 HIS 0.009 0.001 HIS B 928 PHE 0.026 0.001 PHE B1032 TYR 0.019 0.001 TYR A 309 ARG 0.004 0.000 ARG B 420 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 1042) hydrogen bonds : angle 3.65235 ( 3084) covalent geometry : bond 0.00331 (15239) covalent geometry : angle 0.54778 (20710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3652 Ramachandran restraints generated. 1826 Oldfield, 0 Emsley, 1826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 212 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 444 ASN cc_start: 0.7637 (OUTLIER) cc_final: 0.7162 (m110) REVERT: A 483 MET cc_start: 0.8296 (mmp) cc_final: 0.7948 (mmt) REVERT: A 611 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8696 (mm) REVERT: A 1044 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: A 1173 LYS cc_start: 0.3508 (pttm) cc_final: 0.3277 (mttp) REVERT: B 172 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: B 477 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8628 (tt) REVERT: B 611 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8631 (mm) REVERT: B 857 MET cc_start: 0.6229 (mmp) cc_final: 0.5696 (tmm) REVERT: B 1173 LYS cc_start: 0.5602 (mptt) cc_final: 0.4938 (mptt) outliers start: 76 outliers final: 53 residues processed: 256 average time/residue: 0.2226 time to fit residues: 88.8392 Evaluate side-chains 266 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 207 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 643 TRP Chi-restraints excluded: chain A residue 811 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 889 HIS Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 957 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1045 MET Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1096 ILE Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1174 LEU Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 199 MET Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 374 GLN Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 643 TRP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 889 HIS Chi-restraints excluded: chain B residue 948 ILE Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain B residue 989 VAL Chi-restraints excluded: chain B residue 1174 LEU Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 70.6706 > 50: distance: 8 - 14: 19.564 distance: 14 - 15: 50.597 distance: 15 - 18: 41.155 distance: 16 - 17: 56.257 distance: 18 - 19: 38.784 distance: 20 - 21: 15.768 distance: 21 - 22: 17.931 distance: 21 - 24: 24.661 distance: 22 - 23: 12.869 distance: 22 - 28: 41.408 distance: 24 - 25: 40.442 distance: 25 - 27: 45.542 distance: 28 - 29: 40.654 distance: 32 - 33: 39.142 distance: 33 - 34: 57.486 distance: 35 - 36: 55.826 distance: 35 - 41: 38.526 distance: 36 - 37: 40.589 distance: 37 - 38: 40.543 distance: 40 - 41: 40.141 distance: 43 - 44: 33.764 distance: 43 - 46: 30.018 distance: 44 - 45: 8.853 distance: 44 - 48: 34.354 distance: 45 - 75: 59.095 distance: 46 - 47: 41.316 distance: 48 - 49: 32.956 distance: 48 - 54: 30.644 distance: 49 - 50: 40.231 distance: 51 - 86: 39.889 distance: 55 - 56: 39.928 distance: 58 - 91: 34.193 distance: 62 - 63: 12.473 distance: 63 - 64: 40.726 distance: 63 - 65: 10.584 distance: 69 - 97: 34.881 distance: 78 - 104: 33.727 distance: 87 - 90: 40.455 distance: 88 - 89: 43.053 distance: 88 - 91: 34.353 distance: 89 - 112: 28.049