Starting phenix.real_space_refine on Thu Jun 12 12:14:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iff_35415/06_2025/8iff_35415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iff_35415/06_2025/8iff_35415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iff_35415/06_2025/8iff_35415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iff_35415/06_2025/8iff_35415.map" model { file = "/net/cci-nas-00/data/ceres_data/8iff_35415/06_2025/8iff_35415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iff_35415/06_2025/8iff_35415.cif" } resolution = 3.1 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= 0.088 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 104 5.16 5 C 8705 2.51 5 N 2366 2.21 5 O 2523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13698 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6800 Classifications: {'peptide': 868} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 834} Chain breaks: 5 Chain: "B" Number of atoms: 6812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 868, 6812 Classifications: {'peptide': 868} Link IDs: {'PCIS': 3, 'PTRANS': 30, 'TRANS': 834} Chain breaks: 5 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'O6E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.67, per 1000 atoms: 0.56 Number of scatterers: 13698 At special positions: 0 Unit cell: (113.05, 122.4, 139.4, 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 104 16.00 O 2523 8.00 N 2366 7.00 C 8705 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.13 Conformation dependent library (CDL) restraints added in 2.5 seconds 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3264 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 17 sheets defined 39.2% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 128 through 132 Processing helix chain 'A' and resid 134 through 146 Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 196 through 202 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 218 through 235 removed outlier: 3.668A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 321 through 331 Processing helix chain 'A' and resid 380 through 426 removed outlier: 3.970A pdb=" N LYS A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL A 402 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 removed outlier: 3.870A pdb=" N GLN A 435 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 Processing helix chain 'A' and resid 464 through 467 Processing helix chain 'A' and resid 468 through 479 Processing helix chain 'A' and resid 489 through 494 removed outlier: 3.554A pdb=" N ALA A 493 " --> pdb=" O SER A 489 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY A 494 " --> pdb=" O LEU A 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 489 through 494' Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.540A pdb=" N LEU A 501 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY A 502 " --> pdb=" O LEU A 499 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 498 through 502' Processing helix chain 'A' and resid 570 through 588 removed outlier: 4.088A pdb=" N ILE A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 588 " --> pdb=" O ARG A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 787 Processing helix chain 'A' and resid 789 through 794 removed outlier: 4.159A pdb=" N ILE A 794 " --> pdb=" O GLU A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 828 Processing helix chain 'A' and resid 876 through 922 removed outlier: 3.780A pdb=" N ARG A 896 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A 897 " --> pdb=" O ALA A 893 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A 898 " --> pdb=" O VAL A 894 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA A 899 " --> pdb=" O LYS A 895 " (cutoff:3.500A) Proline residue: A 910 - end of helix Processing helix chain 'A' and resid 927 through 948 Processing helix chain 'A' and resid 969 through 980 removed outlier: 4.364A pdb=" N VAL A 973 " --> pdb=" O THR A 969 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 988 removed outlier: 3.528A pdb=" N SER A 985 " --> pdb=" O VAL A 981 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY A 987 " --> pdb=" O MET A 983 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 988 " --> pdb=" O LYS A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1015 removed outlier: 4.133A pdb=" N VAL A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1026 removed outlier: 3.634A pdb=" N PHE A1019 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET A1020 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N MET A1022 " --> pdb=" O PHE A1019 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL A1024 " --> pdb=" O LEU A1021 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A1026 " --> pdb=" O ALA A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1070 Processing helix chain 'A' and resid 1080 through 1082 No H-bonds generated for 'chain 'A' and resid 1080 through 1082' Processing helix chain 'A' and resid 1083 through 1095 removed outlier: 3.825A pdb=" N MET A1087 " --> pdb=" O GLY A1083 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.806A pdb=" N LYS B 76 " --> pdb=" O HIS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 107 removed outlier: 4.143A pdb=" N GLU B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.641A pdb=" N SER B 131 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU B 132 " --> pdb=" O ILE B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 134 through 146 Processing helix chain 'B' and resid 149 through 153 removed outlier: 4.081A pdb=" N LEU B 152 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 201 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 219 through 235 Processing helix chain 'B' and resid 275 through 282 Processing helix chain 'B' and resid 321 through 331 removed outlier: 3.767A pdb=" N MET B 331 " --> pdb=" O TYR B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 401 Processing helix chain 'B' and resid 402 through 414 removed outlier: 3.600A pdb=" N ASN B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 426 Processing helix chain 'B' and resid 429 through 433 removed outlier: 3.657A pdb=" N VAL B 433 " --> pdb=" O LEU B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 442 Processing helix chain 'B' and resid 464 through 479 Processing helix chain 'B' and resid 489 through 494 removed outlier: 3.710A pdb=" N ALA B 493 " --> pdb=" O SER B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 502 removed outlier: 4.428A pdb=" N LEU B 501 " --> pdb=" O ARG B 497 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY B 502 " --> pdb=" O ALA B 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 497 through 502' Processing helix chain 'B' and resid 570 through 588 removed outlier: 3.939A pdb=" N ILE B 576 " --> pdb=" O GLU B 572 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS B 588 " --> pdb=" O ARG B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 787 Processing helix chain 'B' and resid 820 through 832 removed outlier: 3.601A pdb=" N VAL B 824 " --> pdb=" O ASN B 820 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 826 " --> pdb=" O GLY B 822 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N VAL B 829 " --> pdb=" O LEU B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 876 through 922 removed outlier: 3.619A pdb=" N ALA B 889 " --> pdb=" O VAL B 885 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ARG B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR B 892 " --> pdb=" O LEU B 888 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 899 " --> pdb=" O LYS B 895 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS B 904 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG B 905 " --> pdb=" O ALA B 901 " (cutoff:3.500A) Proline residue: B 910 - end of helix Processing helix chain 'B' and resid 927 through 948 removed outlier: 3.900A pdb=" N GLN B 943 " --> pdb=" O LEU B 939 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LEU B 944 " --> pdb=" O CYS B 940 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 945 " --> pdb=" O GLN B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 980 removed outlier: 3.839A pdb=" N THR B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1002 removed outlier: 4.002A pdb=" N MET B1001 " --> pdb=" O GLY B 997 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B1002 " --> pdb=" O GLU B 998 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 997 through 1002' Processing helix chain 'B' and resid 1011 through 1017 Processing helix chain 'B' and resid 1018 through 1020 No H-bonds generated for 'chain 'B' and resid 1018 through 1020' Processing helix chain 'B' and resid 1021 through 1026 removed outlier: 3.688A pdb=" N ASN B1025 " --> pdb=" O LEU B1021 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE B1026 " --> pdb=" O MET B1022 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1021 through 1026' Processing helix chain 'B' and resid 1065 through 1073 removed outlier: 3.547A pdb=" N GLN B1071 " --> pdb=" O PHE B1067 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET B1072 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE B1073 " --> pdb=" O LEU B1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 1080 through 1095 removed outlier: 3.740A pdb=" N LEU B1095 " --> pdb=" O LYS B1091 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 96 through 98 removed outlier: 6.658A pdb=" N ALA A 88 " --> pdb=" O ILE A 97 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269 removed outlier: 3.541A pdb=" N GLY A 250 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA A 241 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N GLU A 255 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL A 239 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N TRP A 366 " --> pdb=" O PHE A 244 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N VAL A 341 " --> pdb=" O TRP A 366 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU A 368 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N MET A 339 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL A 370 " --> pdb=" O LEU A 337 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU A 337 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N HIS A 372 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA A 335 " --> pdb=" O HIS A 372 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 455 through 460 Processing sheet with id=AA4, first strand: chain 'A' and resid 775 through 778 removed outlier: 6.306A pdb=" N GLY A 768 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TRP A 778 " --> pdb=" O ILE A 766 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A 766 " --> pdb=" O TRP A 778 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY A 867 " --> pdb=" O LYS A 858 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 803 through 804 removed outlier: 3.759A pdb=" N GLY A 804 " --> pdb=" O CYS A 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1035 through 1037 removed outlier: 4.259A pdb=" N SER A1110 " --> pdb=" O LEU A1103 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU A1103 " --> pdb=" O SER A1110 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1040 through 1042 removed outlier: 4.040A pdb=" N HIS A1049 " --> pdb=" O ALA A1119 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A1117 " --> pdb=" O ALA A1051 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 80 removed outlier: 6.497A pdb=" N ALA B 88 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR B 99 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU B 86 " --> pdb=" O TYR B 99 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 182 " --> pdb=" O CYS B 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 256 through 257 removed outlier: 3.676A pdb=" N GLY B 250 " --> pdb=" O TYR B 269 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 256 through 257 removed outlier: 6.831A pdb=" N TRP B 366 " --> pdb=" O PHE B 244 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL B 341 " --> pdb=" O TRP B 366 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU B 368 " --> pdb=" O MET B 339 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N MET B 339 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N VAL B 370 " --> pdb=" O LEU B 337 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU B 337 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N HIS B 372 " --> pdb=" O ALA B 335 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA B 335 " --> pdb=" O HIS B 372 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 459 through 460 removed outlier: 3.502A pdb=" N ALA B 448 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY B 484 " --> pdb=" O LYS B 744 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 529 through 531 removed outlier: 3.913A pdb=" N VAL B 530 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU B 559 " --> pdb=" O VAL B 530 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 775 through 778 removed outlier: 6.509A pdb=" N GLY B 768 " --> pdb=" O THR B 776 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N TRP B 778 " --> pdb=" O ILE B 766 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ILE B 766 " --> pdb=" O TRP B 778 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 867 " --> pdb=" O LYS B 858 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 858 " --> pdb=" O GLY B 867 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 967 through 969 Processing sheet with id=AB6, first strand: chain 'B' and resid 991 through 992 removed outlier: 7.408A pdb=" N ARG B 991 " --> pdb=" O LEU B1033 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 1035 through 1042 removed outlier: 3.592A pdb=" N LEU B1057 " --> pdb=" O PHE B1111 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1035 through 1042 removed outlier: 4.166A pdb=" N HIS B1049 " --> pdb=" O ALA B1119 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1629 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: 6.95 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3046 1.33 - 1.45: 2848 1.45 - 1.57: 7890 1.57 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 13952 Sorted by residual: bond pdb=" CAP O6E B1201 " pdb=" CBL O6E B1201 " ideal model delta sigma weight residual 1.448 1.363 0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" CAP O6E A1201 " pdb=" CBL O6E A1201 " ideal model delta sigma weight residual 1.448 1.363 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CAB O6E B1201 " pdb=" CBI O6E B1201 " ideal model delta sigma weight residual 1.449 1.372 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" CAB O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.449 1.383 0.066 2.00e-02 2.50e+03 1.07e+01 bond pdb=" CBC O6E A1201 " pdb=" CBI O6E A1201 " ideal model delta sigma weight residual 1.357 1.410 -0.053 2.00e-02 2.50e+03 7.02e+00 ... (remaining 13947 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 18520 2.10 - 4.20: 275 4.20 - 6.30: 35 6.30 - 8.40: 6 8.40 - 10.50: 3 Bond angle restraints: 18839 Sorted by residual: angle pdb=" CA LYS A 807 " pdb=" CB LYS A 807 " pdb=" CG LYS A 807 " ideal model delta sigma weight residual 114.10 120.57 -6.47 2.00e+00 2.50e-01 1.05e+01 angle pdb=" N ASN A 758 " pdb=" CA ASN A 758 " pdb=" C ASN A 758 " ideal model delta sigma weight residual 109.81 102.75 7.06 2.21e+00 2.05e-01 1.02e+01 angle pdb=" C ALA A 938 " pdb=" N LEU A 939 " pdb=" CA LEU A 939 " ideal model delta sigma weight residual 121.14 115.76 5.38 1.75e+00 3.27e-01 9.45e+00 angle pdb=" CA LEU A 939 " pdb=" CB LEU A 939 " pdb=" CG LEU A 939 " ideal model delta sigma weight residual 116.30 126.80 -10.50 3.50e+00 8.16e-02 9.00e+00 angle pdb=" CA LYS A 807 " pdb=" C LYS A 807 " pdb=" N SER A 808 " ideal model delta sigma weight residual 118.30 114.64 3.66 1.26e+00 6.30e-01 8.44e+00 ... (remaining 18834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 7177 18.00 - 36.01: 998 36.01 - 54.01: 287 54.01 - 72.01: 47 72.01 - 90.02: 22 Dihedral angle restraints: 8531 sinusoidal: 3507 harmonic: 5024 Sorted by residual: dihedral pdb=" CA THR A 969 " pdb=" C THR A 969 " pdb=" N LEU A 970 " pdb=" CA LEU A 970 " ideal model delta harmonic sigma weight residual -180.00 -159.98 -20.02 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA PHE A 871 " pdb=" C PHE A 871 " pdb=" N LEU A 872 " pdb=" CA LEU A 872 " ideal model delta harmonic sigma weight residual -180.00 -161.30 -18.70 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASP A 441 " pdb=" CB ASP A 441 " pdb=" CG ASP A 441 " pdb=" OD1 ASP A 441 " ideal model delta sinusoidal sigma weight residual -30.00 -89.26 59.26 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 8528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1522 0.039 - 0.078: 463 0.078 - 0.117: 121 0.117 - 0.156: 38 0.156 - 0.195: 3 Chirality restraints: 2147 Sorted by residual: chirality pdb=" CBD O6E B1201 " pdb=" CAT O6E B1201 " pdb=" CAX O6E B1201 " pdb=" CBJ O6E B1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.50 -0.20 2.00e-01 2.50e+01 9.54e-01 chirality pdb=" CBD O6E A1201 " pdb=" CAT O6E A1201 " pdb=" CAX O6E A1201 " pdb=" CBJ O6E A1201 " both_signs ideal model delta sigma weight residual False -2.69 -2.52 -0.18 2.00e-01 2.50e+01 7.99e-01 chirality pdb=" CG LEU B 267 " pdb=" CB LEU B 267 " pdb=" CD1 LEU B 267 " pdb=" CD2 LEU B 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 2144 not shown) Planarity restraints: 2400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CAB O6E B1201 " 0.329 2.00e-02 2.50e+03 2.42e-01 1.47e+03 pdb=" CAP O6E B1201 " -0.118 2.00e-02 2.50e+03 pdb=" CAS O6E B1201 " -0.131 2.00e-02 2.50e+03 pdb=" CAW O6E B1201 " -0.191 2.00e-02 2.50e+03 pdb=" CBC O6E B1201 " -0.087 2.00e-02 2.50e+03 pdb=" CBI O6E B1201 " 0.080 2.00e-02 2.50e+03 pdb=" CBL O6E B1201 " 0.491 2.00e-02 2.50e+03 pdb=" CBM O6E B1201 " -0.063 2.00e-02 2.50e+03 pdb=" NAJ O6E B1201 " -0.383 2.00e-02 2.50e+03 pdb=" OAK O6E B1201 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAB O6E A1201 " -0.337 2.00e-02 2.50e+03 2.00e-01 1.00e+03 pdb=" CAP O6E A1201 " 0.178 2.00e-02 2.50e+03 pdb=" CAS O6E A1201 " 0.172 2.00e-02 2.50e+03 pdb=" CAW O6E A1201 " 0.136 2.00e-02 2.50e+03 pdb=" CBC O6E A1201 " 0.080 2.00e-02 2.50e+03 pdb=" CBI O6E A1201 " -0.088 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " -0.409 2.00e-02 2.50e+03 pdb=" CBM O6E A1201 " 0.051 2.00e-02 2.50e+03 pdb=" NAJ O6E A1201 " 0.128 2.00e-02 2.50e+03 pdb=" OAK O6E A1201 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CAA O6E A1201 " -0.051 2.00e-02 2.50e+03 1.72e-01 7.42e+02 pdb=" CAO O6E A1201 " -0.167 2.00e-02 2.50e+03 pdb=" CAP O6E A1201 " -0.295 2.00e-02 2.50e+03 pdb=" CAR O6E A1201 " 0.019 2.00e-02 2.50e+03 pdb=" CAV O6E A1201 " 0.079 2.00e-02 2.50e+03 pdb=" CBB O6E A1201 " 0.010 2.00e-02 2.50e+03 pdb=" CBH O6E A1201 " 0.024 2.00e-02 2.50e+03 pdb=" CBL O6E A1201 " 0.043 2.00e-02 2.50e+03 pdb=" CBO O6E A1201 " -0.070 2.00e-02 2.50e+03 pdb=" NAE O6E A1201 " 0.407 2.00e-02 2.50e+03 ... (remaining 2397 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 359 2.70 - 3.25: 13044 3.25 - 3.80: 20343 3.80 - 4.35: 25515 4.35 - 4.90: 44201 Nonbonded interactions: 103462 Sorted by model distance: nonbonded pdb=" OG SER A 100 " pdb=" OD1 ASN A 102 " model vdw 2.153 3.040 nonbonded pdb=" O ASN A 909 " pdb=" OG SER A 912 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP A 90 " pdb=" OG1 THR A 93 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASN B 330 " pdb=" NE2 HIS B 549 " model vdw 2.256 3.120 nonbonded pdb=" N GLU A 262 " pdb=" OE1 GLU A 262 " model vdw 2.300 3.120 ... (remaining 103457 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 71 through 187 or resid 194 or resid 196 through 1121 or r \ esid 1201)) selection = (chain 'B' and (resid 71 through 187 or resid 195 through 1121 or resid 1201)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 35.220 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 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 : 0.007 0.442 13954 Z= 0.554 Angle : 0.634 10.498 18839 Z= 0.322 Chirality : 0.042 0.195 2147 Planarity : 0.010 0.242 2400 Dihedral : 18.236 90.017 5267 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.27 % Allowed : 29.18 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.43 (0.20), residues: 1712 helix: 1.28 (0.23), residues: 544 sheet: -0.05 (0.30), residues: 303 loop : -1.43 (0.20), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 366 HIS 0.006 0.001 HIS A 467 PHE 0.019 0.002 PHE A 871 TYR 0.016 0.001 TYR A 242 ARG 0.003 0.000 ARG A 497 Details of bonding type rmsd hydrogen bonds : bond 0.12922 ( 582) hydrogen bonds : angle 6.24402 ( 1629) covalent geometry : bond 0.00409 (13952) covalent geometry : angle 0.63369 (18839) Misc. bond : bond 0.43781 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 132 time to evaluate : 1.627 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 THR cc_start: 0.8051 (t) cc_final: 0.7653 (p) outliers start: 4 outliers final: 2 residues processed: 136 average time/residue: 0.3002 time to fit residues: 61.4118 Evaluate side-chains 132 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 ILE Chi-restraints excluded: chain B residue 532 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 44 optimal weight: 0.2980 chunk 87 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1101 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.243651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.146825 restraints weight = 15438.400| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.03 r_work: 0.3540 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.0628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 13954 Z= 0.150 Angle : 0.597 9.464 18839 Z= 0.298 Chirality : 0.042 0.156 2147 Planarity : 0.004 0.041 2400 Dihedral : 6.058 75.360 1938 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 4.46 % Allowed : 25.18 % Favored : 70.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.39 (0.20), residues: 1712 helix: 1.16 (0.22), residues: 566 sheet: -0.03 (0.30), residues: 311 loop : -1.38 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 366 HIS 0.004 0.001 HIS B 172 PHE 0.021 0.002 PHE A 871 TYR 0.017 0.001 TYR A 242 ARG 0.004 0.000 ARG B1090 Details of bonding type rmsd hydrogen bonds : bond 0.04788 ( 582) hydrogen bonds : angle 5.12685 ( 1629) covalent geometry : bond 0.00362 (13952) covalent geometry : angle 0.59710 (18839) Misc. bond : bond 0.00142 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 140 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6040 (OUTLIER) cc_final: 0.5559 (m170) REVERT: A 75 GLN cc_start: 0.6764 (OUTLIER) cc_final: 0.6555 (mt0) REVERT: A 130 ARG cc_start: 0.7808 (mmt180) cc_final: 0.7525 (mmt180) REVERT: A 224 ASP cc_start: 0.8048 (m-30) cc_final: 0.7618 (m-30) REVERT: A 742 MET cc_start: 0.6482 (ttt) cc_final: 0.6045 (ttt) REVERT: B 262 GLU cc_start: 0.7371 (pm20) cc_final: 0.6881 (tt0) REVERT: B 912 SER cc_start: 0.6139 (OUTLIER) cc_final: 0.5882 (t) REVERT: B 915 MET cc_start: 0.3362 (mtm) cc_final: 0.3160 (tpp) REVERT: B 920 MET cc_start: 0.1798 (ptm) cc_final: 0.1435 (mtp) outliers start: 67 outliers final: 42 residues processed: 195 average time/residue: 0.2623 time to fit residues: 79.1294 Evaluate side-chains 180 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 912 SER Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1022 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 13 optimal weight: 0.3980 chunk 145 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 30.0000 chunk 169 optimal weight: 10.0000 chunk 114 optimal weight: 0.5980 chunk 43 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 971 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.245633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.154115 restraints weight = 15531.337| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 4.22 r_work: 0.3531 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.0916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13954 Z= 0.110 Angle : 0.543 9.216 18839 Z= 0.270 Chirality : 0.040 0.140 2147 Planarity : 0.004 0.038 2400 Dihedral : 5.426 68.509 1936 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.06 % Allowed : 25.98 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.17 (0.21), residues: 1712 helix: 1.40 (0.23), residues: 571 sheet: -0.02 (0.30), residues: 315 loop : -1.26 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 366 HIS 0.004 0.001 HIS B 172 PHE 0.017 0.001 PHE A 871 TYR 0.017 0.001 TYR B 752 ARG 0.003 0.000 ARG B1090 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 582) hydrogen bonds : angle 4.77416 ( 1629) covalent geometry : bond 0.00252 (13952) covalent geometry : angle 0.54299 (18839) Misc. bond : bond 0.00147 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 135 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6051 (OUTLIER) cc_final: 0.5615 (m170) REVERT: A 75 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.6514 (mt0) REVERT: A 130 ARG cc_start: 0.7713 (mmt180) cc_final: 0.7473 (mmt180) REVERT: A 338 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8635 (t) REVERT: A 385 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.8200 (t80) REVERT: A 450 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7682 (tt) REVERT: A 480 MET cc_start: 0.8291 (mtm) cc_final: 0.7750 (mpp) REVERT: A 497 ARG cc_start: 0.6689 (mtm110) cc_final: 0.6239 (mtm110) REVERT: A 508 MET cc_start: 0.8268 (ttm) cc_final: 0.8002 (ttm) REVERT: A 742 MET cc_start: 0.6481 (ttt) cc_final: 0.6213 (ttt) REVERT: A 887 ARG cc_start: 0.7784 (ttp-110) cc_final: 0.7449 (ttm110) REVERT: B 325 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7437 (mm) REVERT: B 753 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6981 (mttp) REVERT: B 915 MET cc_start: 0.3151 (mtm) cc_final: 0.2924 (tpp) REVERT: B 920 MET cc_start: 0.1960 (ptm) cc_final: 0.1580 (mtp) outliers start: 61 outliers final: 42 residues processed: 184 average time/residue: 0.2448 time to fit residues: 68.2046 Evaluate side-chains 181 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1022 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 29 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 101 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 159 optimal weight: 0.0870 chunk 81 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.244436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.156887 restraints weight = 15511.389| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 4.00 r_work: 0.3515 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13954 Z= 0.128 Angle : 0.553 8.855 18839 Z= 0.275 Chirality : 0.041 0.152 2147 Planarity : 0.004 0.042 2400 Dihedral : 5.392 66.432 1936 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.86 % Allowed : 24.32 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.21), residues: 1712 helix: 1.39 (0.22), residues: 571 sheet: 0.03 (0.30), residues: 313 loop : -1.23 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 366 HIS 0.004 0.001 HIS B 249 PHE 0.019 0.001 PHE A 871 TYR 0.017 0.001 TYR B 752 ARG 0.002 0.000 ARG B1090 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 582) hydrogen bonds : angle 4.70547 ( 1629) covalent geometry : bond 0.00304 (13952) covalent geometry : angle 0.55264 (18839) Misc. bond : bond 0.00143 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 132 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6145 (OUTLIER) cc_final: 0.5729 (m170) REVERT: A 224 ASP cc_start: 0.8097 (m-30) cc_final: 0.7668 (m-30) REVERT: A 385 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.8078 (t80) REVERT: A 480 MET cc_start: 0.8298 (mtm) cc_final: 0.7771 (mpp) REVERT: A 742 MET cc_start: 0.6601 (ttt) cc_final: 0.6256 (ttt) REVERT: A 887 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7382 (ttm110) REVERT: B 262 GLU cc_start: 0.7401 (pm20) cc_final: 0.6888 (tt0) REVERT: B 325 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7225 (mm) REVERT: B 753 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.7028 (mttp) REVERT: B 920 MET cc_start: 0.2324 (ptm) cc_final: 0.0765 (mmt) REVERT: B 922 GLU cc_start: 0.1238 (OUTLIER) cc_final: -0.0253 (tm-30) REVERT: B 1049 HIS cc_start: 0.0063 (OUTLIER) cc_final: -0.0675 (m170) outliers start: 88 outliers final: 59 residues processed: 200 average time/residue: 0.2461 time to fit residues: 74.0624 Evaluate side-chains 197 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 132 time to evaluate : 1.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 753 LYS Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 982 MET Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 153 optimal weight: 40.0000 chunk 161 optimal weight: 40.0000 chunk 99 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 77 optimal weight: 0.2980 chunk 145 optimal weight: 0.0060 chunk 20 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 overall best weight: 2.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 971 ASN A1101 GLN B 884 HIS B 943 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.242032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144117 restraints weight = 15540.295| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 3.06 r_work: 0.3507 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13954 Z= 0.192 Angle : 0.618 9.546 18839 Z= 0.309 Chirality : 0.043 0.175 2147 Planarity : 0.004 0.044 2400 Dihedral : 5.711 67.846 1936 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 5.60 % Allowed : 25.18 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.20), residues: 1712 helix: 1.08 (0.22), residues: 576 sheet: -0.06 (0.29), residues: 321 loop : -1.31 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 366 HIS 0.005 0.001 HIS B 324 PHE 0.027 0.002 PHE A 916 TYR 0.018 0.002 TYR A 242 ARG 0.003 0.000 ARG A 551 Details of bonding type rmsd hydrogen bonds : bond 0.05189 ( 582) hydrogen bonds : angle 4.90926 ( 1629) covalent geometry : bond 0.00476 (13952) covalent geometry : angle 0.61844 (18839) Misc. bond : bond 0.00141 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 132 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6093 (OUTLIER) cc_final: 0.5768 (m170) REVERT: A 224 ASP cc_start: 0.8195 (m-30) cc_final: 0.7779 (m-30) REVERT: A 385 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8118 (t80) REVERT: A 480 MET cc_start: 0.8292 (mtm) cc_final: 0.7814 (mpp) REVERT: A 742 MET cc_start: 0.6706 (ttt) cc_final: 0.6325 (ttt) REVERT: A 887 ARG cc_start: 0.7672 (ttp-110) cc_final: 0.7349 (ttm110) REVERT: A 983 MET cc_start: 0.1468 (mmm) cc_final: 0.1229 (mtp) REVERT: B 262 GLU cc_start: 0.7443 (pm20) cc_final: 0.6989 (tt0) REVERT: B 325 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7260 (mm) REVERT: B 518 MET cc_start: 0.8702 (ptp) cc_final: 0.8480 (ptm) REVERT: B 558 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6838 (tp) REVERT: B 915 MET cc_start: 0.3197 (mtm) cc_final: 0.2928 (tpp) REVERT: B 920 MET cc_start: 0.2288 (ptm) cc_final: 0.0826 (mmt) REVERT: B 1049 HIS cc_start: 0.0122 (OUTLIER) cc_final: -0.0554 (m170) outliers start: 84 outliers final: 64 residues processed: 198 average time/residue: 0.2463 time to fit residues: 72.9907 Evaluate side-chains 198 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 129 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 513 ILE Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 798 LEU Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 742 MET Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 829 VAL Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 69 optimal weight: 10.0000 chunk 70 optimal weight: 0.0270 chunk 97 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 ASN B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.246323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.157373 restraints weight = 15679.155| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 4.10 r_work: 0.3541 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13954 Z= 0.099 Angle : 0.537 9.822 18839 Z= 0.266 Chirality : 0.040 0.143 2147 Planarity : 0.004 0.049 2400 Dihedral : 5.287 62.659 1936 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.33 % Allowed : 26.05 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.11 (0.21), residues: 1712 helix: 1.43 (0.23), residues: 579 sheet: 0.02 (0.29), residues: 318 loop : -1.24 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 366 HIS 0.003 0.001 HIS A 172 PHE 0.024 0.001 PHE A 916 TYR 0.016 0.001 TYR B 752 ARG 0.002 0.000 ARG B 497 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 582) hydrogen bonds : angle 4.57591 ( 1629) covalent geometry : bond 0.00218 (13952) covalent geometry : angle 0.53707 (18839) Misc. bond : bond 0.00132 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 138 time to evaluate : 1.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6053 (OUTLIER) cc_final: 0.5734 (m170) REVERT: A 128 ASP cc_start: 0.7797 (t0) cc_final: 0.7536 (t0) REVERT: A 130 ARG cc_start: 0.7855 (mmt180) cc_final: 0.7587 (mmt180) REVERT: A 224 ASP cc_start: 0.8145 (m-30) cc_final: 0.7717 (m-30) REVERT: A 338 VAL cc_start: 0.8919 (OUTLIER) cc_final: 0.8663 (t) REVERT: A 385 TYR cc_start: 0.8447 (OUTLIER) cc_final: 0.8108 (t80) REVERT: A 450 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7626 (tt) REVERT: A 480 MET cc_start: 0.8287 (mtm) cc_final: 0.7813 (mpp) REVERT: A 491 HIS cc_start: 0.6317 (OUTLIER) cc_final: 0.5846 (m-70) REVERT: A 742 MET cc_start: 0.6662 (ttt) cc_final: 0.6382 (ttt) REVERT: A 887 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7368 (ttm110) REVERT: A 915 MET cc_start: 0.3774 (mmm) cc_final: 0.3199 (tpp) REVERT: A 983 MET cc_start: 0.1666 (mmm) cc_final: 0.1458 (mtp) REVERT: B 325 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7155 (mm) REVERT: B 338 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8376 (t) REVERT: B 456 ILE cc_start: 0.8981 (mm) cc_final: 0.8578 (mm) REVERT: B 744 LYS cc_start: 0.8346 (mmtm) cc_final: 0.8046 (mptt) REVERT: B 915 MET cc_start: 0.3146 (mtm) cc_final: 0.2834 (tpp) REVERT: B 920 MET cc_start: 0.2416 (ptm) cc_final: 0.1124 (mmm) REVERT: B 922 GLU cc_start: 0.1091 (OUTLIER) cc_final: -0.0392 (tm-30) REVERT: B 1049 HIS cc_start: 0.0059 (OUTLIER) cc_final: -0.0696 (m170) outliers start: 65 outliers final: 44 residues processed: 188 average time/residue: 0.2676 time to fit residues: 76.4802 Evaluate side-chains 184 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 131 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 165 optimal weight: 0.0670 chunk 134 optimal weight: 1.9990 chunk 85 optimal weight: 30.0000 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.242510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.145925 restraints weight = 15553.873| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 3.75 r_work: 0.3506 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13954 Z= 0.177 Angle : 0.615 10.290 18839 Z= 0.305 Chirality : 0.043 0.174 2147 Planarity : 0.004 0.052 2400 Dihedral : 5.616 64.339 1936 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.13 % Allowed : 25.25 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: -0.29 (0.20), residues: 1712 helix: 1.18 (0.22), residues: 577 sheet: -0.06 (0.30), residues: 312 loop : -1.26 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 366 HIS 0.005 0.001 HIS B 249 PHE 0.020 0.002 PHE A 871 TYR 0.018 0.001 TYR A 242 ARG 0.002 0.000 ARG A 551 Details of bonding type rmsd hydrogen bonds : bond 0.04961 ( 582) hydrogen bonds : angle 4.81516 ( 1629) covalent geometry : bond 0.00437 (13952) covalent geometry : angle 0.61489 (18839) Misc. bond : bond 0.00137 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3424 Ramachandran restraints generated. 1712 Oldfield, 0 Emsley, 1712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 132 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6004 (OUTLIER) cc_final: 0.5744 (m170) REVERT: A 128 ASP cc_start: 0.7863 (t0) cc_final: 0.7602 (t0) REVERT: A 224 ASP cc_start: 0.8185 (m-30) cc_final: 0.7776 (m-30) REVERT: A 385 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.8123 (t80) REVERT: A 480 MET cc_start: 0.8336 (mtm) cc_final: 0.7866 (mpp) REVERT: A 491 HIS cc_start: 0.6281 (OUTLIER) cc_final: 0.5813 (m-70) REVERT: A 742 MET cc_start: 0.6682 (ttt) cc_final: 0.6470 (ttt) REVERT: A 887 ARG cc_start: 0.7700 (ttp-110) cc_final: 0.7383 (ttm110) REVERT: A 915 MET cc_start: 0.4199 (mmm) cc_final: 0.3779 (tpp) REVERT: A 983 MET cc_start: 0.1734 (mmm) cc_final: 0.1530 (mtp) REVERT: B 325 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7232 (mm) REVERT: B 456 ILE cc_start: 0.8974 (mm) cc_final: 0.8587 (mm) REVERT: B 558 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6785 (tp) REVERT: B 915 MET cc_start: 0.3111 (mtm) cc_final: 0.2768 (tpp) REVERT: B 920 MET cc_start: 0.2634 (ptm) cc_final: 0.1153 (mmt) REVERT: B 922 GLU cc_start: 0.1175 (OUTLIER) cc_final: -0.0308 (tm-30) REVERT: B 1001 MET cc_start: 0.1693 (mpp) cc_final: -0.0502 (ttp) REVERT: B 1049 HIS cc_start: 0.0092 (OUTLIER) cc_final: -0.0647 (m170) outliers start: 77 outliers final: 61 residues processed: 191 average time/residue: 0.2867 time to fit residues: 83.1603 Evaluate side-chains 198 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 130 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 318 ARG Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 GLU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 467 HIS Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain A residue 520 PHE Chi-restraints excluded: chain A residue 524 SER Chi-restraints excluded: chain A residue 525 HIS Chi-restraints excluded: chain A residue 585 ASN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 806 GLN Chi-restraints excluded: chain A residue 807 LYS Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 851 CYS Chi-restraints excluded: chain A residue 870 CYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 339 MET Chi-restraints excluded: chain B residue 375 THR Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 385 TYR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 421 CYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 532 TRP Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 758 ASN Chi-restraints excluded: chain B residue 766 ILE Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 797 MET Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 819 VAL Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 856 SER Chi-restraints excluded: chain B residue 859 LEU Chi-restraints excluded: chain B residue 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 892 THR Chi-restraints excluded: chain B residue 922 GLU Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/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-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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-5710/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-5710/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-5710/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-5710/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: 56.0055 > 50: distance: 68 - 73: 8.802 distance: 73 - 74: 10.242 distance: 74 - 75: 4.692 distance: 74 - 77: 11.098 distance: 75 - 76: 16.465 distance: 75 - 79: 9.454 distance: 77 - 78: 15.003 distance: 79 - 80: 9.555 distance: 80 - 81: 14.496 distance: 80 - 83: 16.283 distance: 81 - 82: 19.058 distance: 81 - 88: 13.827 distance: 83 - 84: 3.688 distance: 84 - 85: 9.119 distance: 85 - 86: 9.110 distance: 85 - 87: 18.167 distance: 88 - 89: 7.468 distance: 89 - 90: 5.637 distance: 89 - 92: 15.251 distance: 90 - 91: 8.034 distance: 90 - 95: 10.477 distance: 92 - 93: 26.307 distance: 92 - 94: 12.471 distance: 95 - 96: 15.255 distance: 96 - 97: 21.242 distance: 96 - 99: 13.630 distance: 97 - 98: 10.956 distance: 97 - 102: 45.027 distance: 99 - 100: 12.492 distance: 99 - 101: 13.934 distance: 102 - 103: 21.510 distance: 103 - 104: 21.705 distance: 103 - 106: 15.335 distance: 104 - 105: 19.642 distance: 104 - 111: 3.319 distance: 106 - 107: 14.798 distance: 107 - 108: 12.534 distance: 108 - 109: 12.814 distance: 109 - 110: 30.537 distance: 111 - 112: 4.913 distance: 111 - 117: 14.831 distance: 112 - 113: 27.663 distance: 112 - 115: 8.235 distance: 113 - 114: 11.446 distance: 113 - 118: 7.378 distance: 115 - 116: 6.773 distance: 116 - 117: 3.927 distance: 118 - 119: 11.188 distance: 119 - 120: 6.981 distance: 120 - 121: 4.858 distance: 120 - 122: 17.749 distance: 122 - 123: 20.965 distance: 123 - 124: 18.519 distance: 123 - 126: 21.662 distance: 124 - 125: 15.301 distance: 124 - 130: 17.930 distance: 126 - 127: 15.553 distance: 127 - 128: 15.894 distance: 127 - 129: 16.589 distance: 130 - 131: 10.940 distance: 131 - 132: 9.453 distance: 131 - 134: 16.294 distance: 134 - 135: 12.558 distance: 135 - 136: 4.394 distance: 136 - 137: 7.398 distance: 136 - 138: 4.463 distance: 139 - 140: 9.995 distance: 140 - 141: 5.544 distance: 140 - 143: 7.022 distance: 141 - 142: 14.136 distance: 141 - 146: 17.241 distance: 143 - 144: 7.190 distance: 144 - 145: 6.278