Starting phenix.real_space_refine on Mon Dec 30 20:09:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iff_35415/12_2024/8iff_35415.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iff_35415/12_2024/8iff_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_35415/12_2024/8iff_35415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iff_35415/12_2024/8iff_35415.map" model { file = "/net/cci-nas-00/data/ceres_data/8iff_35415/12_2024/8iff_35415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iff_35415/12_2024/8iff_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-5532/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: 7.83, per 1000 atoms: 0.57 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: 3.34 Conformation dependent library (CDL) restraints added in 1.8 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: 1.70 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: 4.79 Time building geometry restraints manager: 3.90 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: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.110 Find NCS groups from input model: 0.610 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.570 ------------------------------------------------------------------------------- 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 : 0.004 0.085 13952 Z= 0.270 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 *********************** 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 : 1.471 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: 0.2696 time to fit residues: 54.2774 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 : 1.416 ------------------------------------------------------------------------------- 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: 5.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 13952 Z= 0.234 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 *********************** 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 : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6069 (OUTLIER) cc_final: 0.5569 (m170) REVERT: A 75 GLN cc_start: 0.6767 (OUTLIER) cc_final: 0.6541 (mt0) REVERT: A 130 ARG cc_start: 0.7842 (mmt180) cc_final: 0.7573 (mmt180) REVERT: A 224 ASP cc_start: 0.8187 (m-30) cc_final: 0.7919 (m-30) REVERT: A 742 MET cc_start: 0.6418 (ttt) cc_final: 0.6096 (ttt) REVERT: B 920 MET cc_start: 0.1845 (ptm) cc_final: 0.1297 (mtp) outliers start: 67 outliers final: 42 residues processed: 195 average time/residue: 0.2369 time to fit residues: 70.6929 Evaluate side-chains 178 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 134 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 129 optimal weight: 0.0980 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 53 optimal weight: 0.0670 chunk 125 optimal weight: 8.9990 overall best weight: 1.6324 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13952 Z= 0.224 Angle : 0.579 9.219 18839 Z= 0.288 Chirality : 0.041 0.155 2147 Planarity : 0.004 0.039 2400 Dihedral : 5.650 71.628 1936 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 5.06 % Allowed : 25.45 % Favored : 69.49 % 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: -0.33 (0.20), residues: 1712 helix: 1.22 (0.22), residues: 570 sheet: -0.07 (0.30), residues: 317 loop : -1.33 (0.21), residues: 825 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 0.019 0.002 PHE A 871 TYR 0.017 0.001 TYR B 752 ARG 0.003 0.000 ARG B1090 *********************** 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 214 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 138 time to evaluate : 1.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6033 (OUTLIER) cc_final: 0.5632 (m170) REVERT: A 130 ARG cc_start: 0.7773 (mmt180) cc_final: 0.7538 (mmt180) REVERT: A 224 ASP cc_start: 0.8222 (m-30) cc_final: 0.7951 (m-30) REVERT: A 385 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.8079 (t80) REVERT: A 450 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7845 (tt) REVERT: A 480 MET cc_start: 0.8062 (mtm) cc_final: 0.7662 (mpp) REVERT: A 887 ARG cc_start: 0.7704 (ttp-110) cc_final: 0.7345 (ttm110) REVERT: B 325 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7564 (mm) REVERT: B 456 ILE cc_start: 0.9069 (mm) cc_final: 0.8849 (mm) REVERT: B 558 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6894 (tp) REVERT: B 753 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7415 (mttp) REVERT: B 920 MET cc_start: 0.2004 (ptm) cc_final: 0.1458 (mtp) REVERT: B 922 GLU cc_start: 0.1244 (OUTLIER) cc_final: -0.0668 (tm-30) REVERT: B 1049 HIS cc_start: -0.0783 (OUTLIER) cc_final: -0.1959 (m170) outliers start: 76 outliers final: 55 residues processed: 200 average time/residue: 0.2465 time to fit residues: 74.4189 Evaluate side-chains 197 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 134 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS 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 402 VAL 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 513 ILE 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 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 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 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 418 THR 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 17 optimal weight: 0.0270 chunk 74 optimal weight: 40.0000 chunk 105 optimal weight: 2.9990 chunk 157 optimal weight: 9.9990 chunk 166 optimal weight: 50.0000 chunk 82 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- 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 ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13952 Z= 0.221 Angle : 0.570 9.091 18839 Z= 0.284 Chirality : 0.041 0.157 2147 Planarity : 0.004 0.042 2400 Dihedral : 5.533 68.846 1936 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 5.93 % Allowed : 25.18 % Favored : 68.89 % 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: -0.26 (0.20), residues: 1712 helix: 1.28 (0.22), residues: 570 sheet: -0.03 (0.30), residues: 317 loop : -1.30 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 366 HIS 0.004 0.001 HIS B 249 PHE 0.019 0.002 PHE A 871 TYR 0.016 0.001 TYR A 242 ARG 0.002 0.000 ARG B1090 *********************** 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 222 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 133 time to evaluate : 1.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6075 (OUTLIER) cc_final: 0.5687 (m170) REVERT: A 130 ARG cc_start: 0.7703 (mmt180) cc_final: 0.7496 (mmt180) REVERT: A 224 ASP cc_start: 0.8277 (m-30) cc_final: 0.7991 (m-30) REVERT: A 385 TYR cc_start: 0.8482 (OUTLIER) cc_final: 0.8091 (t80) REVERT: A 480 MET cc_start: 0.8036 (mtm) cc_final: 0.7662 (mpp) REVERT: A 508 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7880 (ttm) REVERT: A 887 ARG cc_start: 0.7711 (ttp-110) cc_final: 0.7354 (ttm110) REVERT: B 296 LYS cc_start: 0.6994 (OUTLIER) cc_final: 0.6764 (tptp) REVERT: B 325 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7574 (mm) REVERT: B 338 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8583 (t) REVERT: B 753 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7369 (mttp) REVERT: B 920 MET cc_start: 0.2287 (ptm) cc_final: 0.0222 (mmt) REVERT: B 965 MET cc_start: -0.1723 (mmt) cc_final: -0.1930 (mmt) outliers start: 89 outliers final: 60 residues processed: 206 average time/residue: 0.2506 time to fit residues: 77.7183 Evaluate side-chains 199 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 132 time to evaluate : 1.562 ------------------------------------------------------------------------------- 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 402 VAL Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 508 MET 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 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 227 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 296 LYS 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 418 THR 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 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 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 982 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 6.9990 chunk 94 optimal weight: 0.9990 chunk 2 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 40.0000 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 ASN A1101 GLN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13952 Z= 0.234 Angle : 0.580 9.442 18839 Z= 0.289 Chirality : 0.042 0.159 2147 Planarity : 0.004 0.044 2400 Dihedral : 5.552 67.360 1936 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 5.66 % Allowed : 25.12 % 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: -0.31 (0.20), residues: 1712 helix: 1.17 (0.22), residues: 577 sheet: -0.02 (0.29), residues: 317 loop : -1.31 (0.21), residues: 818 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 0.022 0.002 PHE A 916 TYR 0.017 0.001 TYR A 242 ARG 0.002 0.000 ARG B1090 *********************** 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 215 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 130 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6072 (OUTLIER) cc_final: 0.5745 (m170) REVERT: A 130 ARG cc_start: 0.7642 (mmt180) cc_final: 0.7421 (mmt180) REVERT: A 224 ASP cc_start: 0.8298 (m-30) cc_final: 0.8039 (m-30) REVERT: A 385 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.8058 (t80) REVERT: A 440 MET cc_start: 0.8534 (ttm) cc_final: 0.8329 (mtp) REVERT: A 450 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7780 (tt) REVERT: A 480 MET cc_start: 0.8046 (mtm) cc_final: 0.7722 (mpp) REVERT: A 887 ARG cc_start: 0.7668 (ttp-110) cc_final: 0.7339 (ttm110) REVERT: A 983 MET cc_start: 0.0918 (mmm) cc_final: 0.0693 (mtp) REVERT: B 296 LYS cc_start: 0.6991 (OUTLIER) cc_final: 0.6763 (tptp) REVERT: B 558 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6827 (tp) REVERT: B 744 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8176 (mptt) REVERT: B 753 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7392 (mttp) REVERT: B 915 MET cc_start: 0.1733 (mtm) cc_final: 0.1465 (tpt) REVERT: B 920 MET cc_start: 0.2301 (ptm) cc_final: 0.0292 (mmt) REVERT: B 1049 HIS cc_start: -0.0539 (OUTLIER) cc_final: -0.1775 (m170) outliers start: 85 outliers final: 65 residues processed: 201 average time/residue: 0.2354 time to fit residues: 71.4437 Evaluate side-chains 200 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 128 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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 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 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 450 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 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 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 239 VAL Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS 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 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 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 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 55 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 166 optimal weight: 50.0000 chunk 138 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 160 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 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 971 ASN ** B 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 884 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13952 Z= 0.386 Angle : 0.687 14.029 18839 Z= 0.341 Chirality : 0.046 0.233 2147 Planarity : 0.005 0.047 2400 Dihedral : 6.063 69.433 1936 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 6.33 % Allowed : 25.18 % Favored : 68.49 % 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: -0.61 (0.20), residues: 1712 helix: 0.87 (0.22), residues: 570 sheet: -0.30 (0.29), residues: 333 loop : -1.38 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 366 HIS 0.007 0.001 HIS B 249 PHE 0.023 0.002 PHE A 916 TYR 0.019 0.002 TYR A 242 ARG 0.003 0.000 ARG A 551 *********************** 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 228 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 133 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.5986 (OUTLIER) cc_final: 0.5748 (m170) REVERT: A 128 ASP cc_start: 0.7826 (t0) cc_final: 0.7556 (t0) REVERT: A 130 ARG cc_start: 0.7768 (mmt180) cc_final: 0.7450 (mmt180) REVERT: A 224 ASP cc_start: 0.8341 (m-30) cc_final: 0.8079 (m-30) REVERT: A 385 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.8026 (t80) REVERT: A 480 MET cc_start: 0.8060 (mtm) cc_final: 0.7631 (mpp) REVERT: A 491 HIS cc_start: 0.6328 (OUTLIER) cc_final: 0.5783 (m-70) REVERT: A 887 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7329 (ttm110) REVERT: A 915 MET cc_start: 0.3923 (mmm) cc_final: 0.3108 (tpp) REVERT: B 214 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8191 (mp) REVERT: B 296 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6785 (tptp) REVERT: B 497 ARG cc_start: 0.6725 (ttp-170) cc_final: 0.6152 (ttt180) REVERT: B 753 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7567 (mttp) REVERT: B 915 MET cc_start: 0.1797 (mtm) cc_final: 0.1225 (tpp) REVERT: B 920 MET cc_start: 0.2483 (ptm) cc_final: 0.0436 (mmt) REVERT: B 922 GLU cc_start: 0.0982 (OUTLIER) cc_final: -0.0630 (tm-30) REVERT: B 1049 HIS cc_start: -0.0292 (OUTLIER) cc_final: -0.1638 (m90) outliers start: 95 outliers final: 72 residues processed: 209 average time/residue: 0.2505 time to fit residues: 78.2555 Evaluate side-chains 213 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 133 time to evaluate : 1.529 ------------------------------------------------------------------------------- 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 185 VAL 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 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 491 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 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 798 LEU 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 214 LEU Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS 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 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 753 LYS 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 829 VAL Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 843 THR 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 877 HIS 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 1020 MET 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 18 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 165 optimal weight: 0.0770 chunk 103 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 971 ASN B 245 HIS B 884 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13952 Z= 0.159 Angle : 0.563 12.005 18839 Z= 0.278 Chirality : 0.040 0.182 2147 Planarity : 0.004 0.052 2400 Dihedral : 5.508 64.991 1936 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.53 % Allowed : 26.78 % Favored : 68.69 % 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: -0.26 (0.20), residues: 1712 helix: 1.33 (0.23), residues: 572 sheet: -0.01 (0.29), residues: 317 loop : -1.35 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 366 HIS 0.003 0.001 HIS B 172 PHE 0.019 0.001 PHE A 916 TYR 0.014 0.001 TYR B 752 ARG 0.002 0.000 ARG B 497 *********************** 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 202 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 134 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6010 (OUTLIER) cc_final: 0.5781 (m170) REVERT: A 128 ASP cc_start: 0.7880 (t0) cc_final: 0.7598 (t0) REVERT: A 130 ARG cc_start: 0.7599 (mmt180) cc_final: 0.7328 (mmt180) REVERT: A 224 ASP cc_start: 0.8277 (m-30) cc_final: 0.8005 (m-30) REVERT: A 338 VAL cc_start: 0.8801 (OUTLIER) cc_final: 0.8559 (t) REVERT: A 385 TYR cc_start: 0.8430 (OUTLIER) cc_final: 0.8055 (t80) REVERT: A 480 MET cc_start: 0.8052 (mtm) cc_final: 0.7575 (mpp) REVERT: A 491 HIS cc_start: 0.6359 (OUTLIER) cc_final: 0.5858 (m-70) REVERT: A 508 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7972 (ttm) REVERT: A 887 ARG cc_start: 0.7655 (ttp-110) cc_final: 0.7294 (ttm110) REVERT: A 915 MET cc_start: 0.4254 (mmm) cc_final: 0.3620 (tpp) REVERT: A 948 LEU cc_start: 0.4905 (OUTLIER) cc_final: 0.4485 (tt) REVERT: B 296 LYS cc_start: 0.6979 (OUTLIER) cc_final: 0.6735 (tptp) REVERT: B 299 ARG cc_start: 0.6864 (OUTLIER) cc_final: 0.6291 (ptm160) REVERT: B 558 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6816 (tp) REVERT: B 753 LYS cc_start: 0.7569 (OUTLIER) cc_final: 0.7341 (mttp) REVERT: B 915 MET cc_start: 0.1778 (mtm) cc_final: 0.1303 (tpp) REVERT: B 920 MET cc_start: 0.2459 (ptm) cc_final: 0.0745 (mmm) REVERT: B 922 GLU cc_start: 0.1213 (OUTLIER) cc_final: -0.0539 (tm-30) outliers start: 68 outliers final: 49 residues processed: 188 average time/residue: 0.2498 time to fit residues: 69.1122 Evaluate side-chains 188 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 128 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 85 CYS 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 257 THR 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 385 TYR Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 491 HIS Chi-restraints excluded: chain A residue 508 MET 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 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 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 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 299 ARG 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 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 558 LEU 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 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 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 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 ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 0.4980 chunk 130 optimal weight: 0.0970 chunk 150 optimal weight: 0.0570 chunk 158 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13952 Z= 0.155 Angle : 0.556 11.203 18839 Z= 0.274 Chirality : 0.040 0.169 2147 Planarity : 0.004 0.055 2400 Dihedral : 5.302 60.193 1936 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.53 % Allowed : 26.92 % Favored : 68.55 % 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: -0.13 (0.21), residues: 1712 helix: 1.48 (0.23), residues: 580 sheet: 0.03 (0.30), residues: 301 loop : -1.30 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 366 HIS 0.003 0.001 HIS A 172 PHE 0.016 0.001 PHE A 916 TYR 0.015 0.001 TYR B 752 ARG 0.002 0.000 ARG B 497 *********************** REFINEMENT MACRO_CYCLE 8 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 198 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 130 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.5754 (m170) REVERT: A 128 ASP cc_start: 0.7860 (t0) cc_final: 0.7526 (t0) REVERT: A 224 ASP cc_start: 0.8275 (m-30) cc_final: 0.7988 (m-30) REVERT: A 338 VAL cc_start: 0.8791 (OUTLIER) cc_final: 0.8560 (t) REVERT: A 385 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.8149 (t80) REVERT: A 450 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7826 (tt) REVERT: A 480 MET cc_start: 0.8047 (mtm) cc_final: 0.7515 (mpp) REVERT: A 491 HIS cc_start: 0.6401 (OUTLIER) cc_final: 0.5942 (m-70) REVERT: A 508 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7982 (ttm) REVERT: A 887 ARG cc_start: 0.7654 (ttp-110) cc_final: 0.7303 (ttm110) REVERT: A 915 MET cc_start: 0.4383 (mmm) cc_final: 0.3797 (tpp) REVERT: A 948 LEU cc_start: 0.4928 (OUTLIER) cc_final: 0.4497 (tt) REVERT: A 983 MET cc_start: 0.2074 (mtp) cc_final: 0.1476 (tmm) REVERT: B 296 LYS cc_start: 0.6946 (OUTLIER) cc_final: 0.6708 (tptp) REVERT: B 299 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6296 (ptm160) REVERT: B 338 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8647 (t) REVERT: B 753 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7319 (mttp) REVERT: B 920 MET cc_start: 0.2614 (ptm) cc_final: 0.0983 (mmm) REVERT: B 922 GLU cc_start: 0.1123 (OUTLIER) cc_final: -0.0604 (tm-30) REVERT: B 1001 MET cc_start: 0.2566 (mpp) cc_final: -0.0352 (ttp) outliers start: 68 outliers final: 52 residues processed: 183 average time/residue: 0.2590 time to fit residues: 70.1643 Evaluate side-chains 191 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 127 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 THR 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 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 508 MET 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 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 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 982 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS 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 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 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 865 VAL Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 888 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 20.0000 chunk 158 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13952 Z= 0.256 Angle : 0.615 11.528 18839 Z= 0.304 Chirality : 0.042 0.175 2147 Planarity : 0.004 0.055 2400 Dihedral : 5.550 61.039 1936 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 5.13 % Allowed : 26.38 % Favored : 68.49 % 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: 1.22 (0.22), residues: 584 sheet: 0.00 (0.30), residues: 305 loop : -1.34 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 366 HIS 0.005 0.001 HIS B 249 PHE 0.020 0.002 PHE A 871 TYR 0.017 0.001 TYR A 242 ARG 0.002 0.000 ARG B 497 *********************** REFINEMENT MACRO_CYCLE 9 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 205 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 128 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6042 (OUTLIER) cc_final: 0.5813 (m170) REVERT: A 128 ASP cc_start: 0.7839 (t0) cc_final: 0.7539 (t0) REVERT: A 224 ASP cc_start: 0.8310 (m-30) cc_final: 0.8046 (m-30) REVERT: A 385 TYR cc_start: 0.8522 (OUTLIER) cc_final: 0.8079 (t80) REVERT: A 450 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7855 (tt) REVERT: A 480 MET cc_start: 0.8043 (mtm) cc_final: 0.7557 (mpp) REVERT: A 887 ARG cc_start: 0.7646 (ttp-110) cc_final: 0.7308 (ttm110) REVERT: A 915 MET cc_start: 0.4600 (mmm) cc_final: 0.4067 (tpp) REVERT: A 948 LEU cc_start: 0.4902 (OUTLIER) cc_final: 0.4467 (tt) REVERT: A 983 MET cc_start: 0.2335 (mtp) cc_final: 0.1613 (tmm) REVERT: B 296 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.6757 (tptp) REVERT: B 299 ARG cc_start: 0.6924 (OUTLIER) cc_final: 0.6308 (ptm160) REVERT: B 753 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7411 (mttp) REVERT: B 920 MET cc_start: 0.2775 (ptm) cc_final: 0.0837 (mmp) REVERT: B 922 GLU cc_start: 0.1092 (OUTLIER) cc_final: -0.0620 (tm-30) REVERT: B 1001 MET cc_start: 0.2642 (mpp) cc_final: -0.0268 (ttp) outliers start: 77 outliers final: 60 residues processed: 187 average time/residue: 0.2549 time to fit residues: 71.3782 Evaluate side-chains 194 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 126 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 THR 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 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 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 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 982 MET Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 323 CYS 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 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 748 ILE Chi-restraints excluded: chain B residue 753 LYS 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 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 1020 MET Chi-restraints excluded: chain B residue 1022 MET Chi-restraints excluded: chain B residue 1049 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 113 optimal weight: 0.9980 chunk 171 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 145 optimal weight: 0.0570 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13952 Z= 0.151 Angle : 0.558 10.357 18839 Z= 0.275 Chirality : 0.040 0.161 2147 Planarity : 0.004 0.056 2400 Dihedral : 5.244 57.220 1936 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.26 % Allowed : 27.25 % Favored : 68.49 % 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: -0.13 (0.21), residues: 1712 helix: 1.50 (0.23), residues: 580 sheet: -0.06 (0.30), residues: 307 loop : -1.28 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 366 HIS 0.003 0.001 HIS B 172 PHE 0.015 0.001 PHE A 916 TYR 0.016 0.001 TYR B 752 ARG 0.003 0.000 ARG A 523 ********************** REFINEMENT MACRO_CYCLE 10 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 190 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 126 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 HIS cc_start: 0.6047 (OUTLIER) cc_final: 0.5829 (m170) REVERT: A 128 ASP cc_start: 0.7780 (t0) cc_final: 0.7457 (t0) REVERT: A 224 ASP cc_start: 0.8275 (m-30) cc_final: 0.7990 (m-30) REVERT: A 338 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8557 (t) REVERT: A 385 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.8147 (t80) REVERT: A 450 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7799 (tt) REVERT: A 480 MET cc_start: 0.8044 (mtm) cc_final: 0.7514 (mpp) REVERT: A 491 HIS cc_start: 0.6427 (OUTLIER) cc_final: 0.5960 (m-70) REVERT: A 887 ARG cc_start: 0.7649 (ttp-110) cc_final: 0.7310 (ttm110) REVERT: A 915 MET cc_start: 0.4608 (mmm) cc_final: 0.4109 (tpp) REVERT: A 948 LEU cc_start: 0.4929 (OUTLIER) cc_final: 0.4498 (tt) REVERT: A 983 MET cc_start: 0.2233 (mtp) cc_final: 0.1513 (tmm) REVERT: B 296 LYS cc_start: 0.6927 (OUTLIER) cc_final: 0.6694 (tptp) REVERT: B 299 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6289 (ptm160) REVERT: B 338 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8654 (t) REVERT: B 470 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7438 (mm-30) REVERT: B 753 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7284 (mttp) REVERT: B 887 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6584 (tmm-80) REVERT: B 920 MET cc_start: 0.2772 (ptm) cc_final: 0.1123 (mmm) REVERT: B 922 GLU cc_start: 0.1437 (OUTLIER) cc_final: -0.0328 (tm-30) REVERT: B 1001 MET cc_start: 0.2307 (mpp) cc_final: -0.0219 (ttp) outliers start: 64 outliers final: 49 residues processed: 178 average time/residue: 0.2716 time to fit residues: 71.3843 Evaluate side-chains 186 residues out of total 1501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 125 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 HIS Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 251 GLU Chi-restraints excluded: chain A residue 257 THR 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 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 519 ILE 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 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 171 ILE Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 299 ARG Chi-restraints excluded: chain B residue 312 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 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 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 865 VAL Chi-restraints excluded: chain B residue 870 CYS Chi-restraints excluded: chain B residue 887 ARG Chi-restraints excluded: chain B residue 888 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 6.9990 chunk 125 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 136 optimal weight: 0.0000 chunk 57 optimal weight: 1.9990 chunk 140 optimal weight: 0.0010 chunk 17 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.5770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 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 = 0.4697 r_free = 0.4697 target = 0.247395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.157593 restraints weight = 15543.794| |-----------------------------------------------------------------------------| r_work (start): 0.3874 rms_B_bonded: 3.91 r_work: 0.3622 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13952 Z= 0.143 Angle : 0.543 10.078 18839 Z= 0.268 Chirality : 0.039 0.149 2147 Planarity : 0.004 0.055 2400 Dihedral : 4.961 56.231 1936 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.13 % Allowed : 27.38 % Favored : 68.49 % 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: -0.02 (0.21), residues: 1712 helix: 1.62 (0.23), residues: 580 sheet: -0.00 (0.30), residues: 307 loop : -1.23 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 366 HIS 0.003 0.001 HIS A 172 PHE 0.014 0.001 PHE A 916 TYR 0.016 0.001 TYR B 752 ARG 0.003 0.000 ARG A 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2778.23 seconds wall clock time: 51 minutes 45.46 seconds (3105.46 seconds total)