Starting phenix.real_space_refine on Tue May 27 08:42:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vaz_43107/05_2025/8vaz_43107.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vaz_43107/05_2025/8vaz_43107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vaz_43107/05_2025/8vaz_43107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vaz_43107/05_2025/8vaz_43107.map" model { file = "/net/cci-nas-00/data/ceres_data/8vaz_43107/05_2025/8vaz_43107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vaz_43107/05_2025/8vaz_43107.cif" } resolution = 2.82 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= 0.006 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 192 5.16 5 C 19068 2.51 5 N 4820 2.21 5 O 5320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29404 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7097 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 27, 'TRANS': 862} Chain breaks: 3 Chain: "B" Number of atoms: 7097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7097 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 27, 'TRANS': 862} Chain breaks: 3 Chain: "C" Number of atoms: 7097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7097 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 27, 'TRANS': 862} Chain breaks: 3 Chain: "D" Number of atoms: 7097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 7097 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 27, 'TRANS': 862} Chain breaks: 3 Chain: "E" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 253 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "F" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 253 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "G" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 253 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "H" Number of atoms: 253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 253 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.06, per 1000 atoms: 0.58 Number of scatterers: 29404 At special positions: 0 Unit cell: (160.92, 160.92, 135, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 192 16.00 O 5320 8.00 N 4820 7.00 C 19068 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.41 Conformation dependent library (CDL) restraints added in 3.7 seconds 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7016 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 24 sheets defined 56.9% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 21 through 46 removed outlier: 3.848A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 147 through 170 removed outlier: 3.800A pdb=" N GLN A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 179 Processing helix chain 'A' and resid 180 through 200 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 229 through 260 Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 297 through 327 Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 352 through 364 Processing helix chain 'A' and resid 384 through 394 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 Processing helix chain 'A' and resid 462 through 472 removed outlier: 3.597A pdb=" N ASN A 465 " --> pdb=" O GLN A 462 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS A 466 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA A 467 " --> pdb=" O HIS A 464 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE A 472 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 Processing helix chain 'A' and resid 486 through 500 Processing helix chain 'A' and resid 502 through 511 Processing helix chain 'A' and resid 523 through 533 removed outlier: 4.057A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 549 through 560 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 699 through 704 removed outlier: 4.135A pdb=" N VAL A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 739 Processing helix chain 'A' and resid 740 through 743 removed outlier: 3.817A pdb=" N ALA A 743 " --> pdb=" O PRO A 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 740 through 743' Processing helix chain 'A' and resid 759 through 767 removed outlier: 3.556A pdb=" N LEU A 763 " --> pdb=" O SER A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 812 through 816 Processing helix chain 'A' and resid 817 through 829 Processing helix chain 'A' and resid 872 through 876 removed outlier: 4.005A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 892 removed outlier: 3.617A pdb=" N ASN A 887 " --> pdb=" O ASN A 884 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 892 " --> pdb=" O GLN A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 905 Processing helix chain 'A' and resid 906 through 911 Processing helix chain 'A' and resid 917 through 930 removed outlier: 4.016A pdb=" N ASP A 921 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 930 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 942 removed outlier: 4.104A pdb=" N THR A 935 " --> pdb=" O ASP A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 957 Processing helix chain 'A' and resid 965 through 973 removed outlier: 3.909A pdb=" N ASP A 973 " --> pdb=" O LEU A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1007 removed outlier: 3.577A pdb=" N LEU A 999 " --> pdb=" O CYS A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1021 No H-bonds generated for 'chain 'A' and resid 1019 through 1021' Processing helix chain 'B' and resid 21 through 46 removed outlier: 3.804A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 Processing helix chain 'B' and resid 109 through 134 Processing helix chain 'B' and resid 147 through 170 removed outlier: 3.792A pdb=" N GLN B 151 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 179 Processing helix chain 'B' and resid 180 through 200 Proline residue: B 191 - end of helix Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 229 through 260 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.500A pdb=" N ASN B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 297 through 327 Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 352 through 364 Processing helix chain 'B' and resid 384 through 394 Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 462 through 472 removed outlier: 3.595A pdb=" N ASN B 465 " --> pdb=" O GLN B 462 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 466 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA B 467 " --> pdb=" O HIS B 464 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE B 472 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 Processing helix chain 'B' and resid 486 through 500 Processing helix chain 'B' and resid 502 through 511 Processing helix chain 'B' and resid 523 through 533 removed outlier: 4.058A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N SER B 533 " --> pdb=" O LEU B 529 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 546 Processing helix chain 'B' and resid 549 through 560 Processing helix chain 'B' and resid 603 through 609 Processing helix chain 'B' and resid 699 through 704 removed outlier: 4.137A pdb=" N VAL B 703 " --> pdb=" O GLU B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 739 Processing helix chain 'B' and resid 740 through 743 removed outlier: 3.816A pdb=" N ALA B 743 " --> pdb=" O PRO B 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 740 through 743' Processing helix chain 'B' and resid 759 through 767 removed outlier: 3.553A pdb=" N LEU B 763 " --> pdb=" O SER B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 770 No H-bonds generated for 'chain 'B' and resid 768 through 770' Processing helix chain 'B' and resid 785 through 792 Processing helix chain 'B' and resid 812 through 816 Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'B' and resid 872 through 876 removed outlier: 4.008A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 892 removed outlier: 3.620A pdb=" N ASN B 887 " --> pdb=" O ASN B 884 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 892 " --> pdb=" O GLN B 889 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 905 Processing helix chain 'B' and resid 906 through 911 Processing helix chain 'B' and resid 917 through 930 removed outlier: 4.017A pdb=" N ASP B 921 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET B 924 " --> pdb=" O LEU B 920 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN B 930 " --> pdb=" O ALA B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 942 removed outlier: 4.122A pdb=" N THR B 935 " --> pdb=" O ASP B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 957 Processing helix chain 'B' and resid 965 through 973 removed outlier: 3.909A pdb=" N ASP B 973 " --> pdb=" O LEU B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 995 through 1007 removed outlier: 3.575A pdb=" N LEU B 999 " --> pdb=" O CYS B 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 46 removed outlier: 3.819A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLY C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 147 through 170 removed outlier: 3.787A pdb=" N GLN C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 179 Processing helix chain 'C' and resid 180 through 200 Proline residue: C 191 - end of helix Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 229 through 260 Processing helix chain 'C' and resid 261 through 265 Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 297 through 327 Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 352 through 364 Processing helix chain 'C' and resid 384 through 394 Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 Processing helix chain 'C' and resid 462 through 472 removed outlier: 3.593A pdb=" N ASN C 465 " --> pdb=" O GLN C 462 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS C 466 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA C 467 " --> pdb=" O HIS C 464 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 472 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 Processing helix chain 'C' and resid 486 through 500 Processing helix chain 'C' and resid 502 through 511 Processing helix chain 'C' and resid 523 through 533 removed outlier: 4.065A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER C 533 " --> pdb=" O LEU C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 560 Processing helix chain 'C' and resid 603 through 609 Processing helix chain 'C' and resid 699 through 704 removed outlier: 4.137A pdb=" N VAL C 703 " --> pdb=" O GLU C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 739 Processing helix chain 'C' and resid 740 through 743 removed outlier: 3.816A pdb=" N ALA C 743 " --> pdb=" O PRO C 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 740 through 743' Processing helix chain 'C' and resid 759 through 767 removed outlier: 3.552A pdb=" N LEU C 763 " --> pdb=" O SER C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 770 No H-bonds generated for 'chain 'C' and resid 768 through 770' Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 812 through 816 Processing helix chain 'C' and resid 817 through 829 Processing helix chain 'C' and resid 872 through 876 removed outlier: 4.010A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 892 removed outlier: 3.624A pdb=" N ASN C 887 " --> pdb=" O ASN C 884 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C 892 " --> pdb=" O GLN C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 902 through 905 Processing helix chain 'C' and resid 906 through 911 Processing helix chain 'C' and resid 917 through 930 removed outlier: 4.014A pdb=" N ASP C 921 " --> pdb=" O VAL C 917 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET C 924 " --> pdb=" O LEU C 920 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 942 removed outlier: 4.122A pdb=" N THR C 935 " --> pdb=" O ASP C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 957 Processing helix chain 'C' and resid 965 through 973 removed outlier: 3.908A pdb=" N ASP C 973 " --> pdb=" O LEU C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 995 through 1007 removed outlier: 3.579A pdb=" N LEU C 999 " --> pdb=" O CYS C 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 46 removed outlier: 3.826A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 105 Processing helix chain 'D' and resid 109 through 134 Processing helix chain 'D' and resid 147 through 170 removed outlier: 3.787A pdb=" N GLN D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 180 through 200 Proline residue: D 191 - end of helix Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 229 through 260 Processing helix chain 'D' and resid 261 through 265 Processing helix chain 'D' and resid 273 through 286 Processing helix chain 'D' and resid 297 through 327 Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 352 through 364 Processing helix chain 'D' and resid 384 through 394 Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 432 through 451 Processing helix chain 'D' and resid 462 through 472 removed outlier: 3.596A pdb=" N ASN D 465 " --> pdb=" O GLN D 462 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS D 466 " --> pdb=" O TYR D 463 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA D 467 " --> pdb=" O HIS D 464 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE D 472 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 480 Processing helix chain 'D' and resid 486 through 500 Processing helix chain 'D' and resid 502 through 511 Processing helix chain 'D' and resid 523 through 533 removed outlier: 4.062A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER D 533 " --> pdb=" O LEU D 529 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 546 Processing helix chain 'D' and resid 549 through 560 Processing helix chain 'D' and resid 603 through 609 Processing helix chain 'D' and resid 699 through 704 removed outlier: 4.137A pdb=" N VAL D 703 " --> pdb=" O GLU D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 739 Processing helix chain 'D' and resid 740 through 743 removed outlier: 3.819A pdb=" N ALA D 743 " --> pdb=" O PRO D 740 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 740 through 743' Processing helix chain 'D' and resid 759 through 767 removed outlier: 3.551A pdb=" N LEU D 763 " --> pdb=" O SER D 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 770 No H-bonds generated for 'chain 'D' and resid 768 through 770' Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 812 through 816 Processing helix chain 'D' and resid 817 through 829 Processing helix chain 'D' and resid 872 through 876 removed outlier: 4.004A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 892 removed outlier: 3.622A pdb=" N ASN D 887 " --> pdb=" O ASN D 884 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP D 892 " --> pdb=" O GLN D 889 " (cutoff:3.500A) Processing helix chain 'D' and resid 902 through 905 Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 917 through 930 removed outlier: 4.014A pdb=" N ASP D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET D 924 " --> pdb=" O LEU D 920 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN D 930 " --> pdb=" O ALA D 926 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 942 removed outlier: 4.123A pdb=" N THR D 935 " --> pdb=" O ASP D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 957 Processing helix chain 'D' and resid 965 through 973 removed outlier: 3.907A pdb=" N ASP D 973 " --> pdb=" O LEU D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 995 through 1007 removed outlier: 3.579A pdb=" N LEU D 999 " --> pdb=" O CYS D 995 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 293 removed outlier: 5.040A pdb=" N GLY E 269 " --> pdb=" O VAL E 265 " (cutoff:3.500A) Proline residue: E 270 - end of helix Processing helix chain 'F' and resid 259 through 293 removed outlier: 4.869A pdb=" N GLY F 269 " --> pdb=" O VAL F 265 " (cutoff:3.500A) Proline residue: F 270 - end of helix Processing helix chain 'G' and resid 259 through 293 removed outlier: 5.008A pdb=" N GLY G 269 " --> pdb=" O VAL G 265 " (cutoff:3.500A) Proline residue: G 270 - end of helix Processing helix chain 'H' and resid 259 through 293 removed outlier: 4.616A pdb=" N GLY H 269 " --> pdb=" O VAL H 265 " (cutoff:3.500A) Proline residue: H 270 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 141 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 401 removed outlier: 8.671A pdb=" N GLU A 399 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE A 375 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N TYR A 401 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE A 377 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 458 " --> pdb=" O ILE A 484 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 535 through 540 removed outlier: 6.875A pdb=" N LEU A 594 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ILE A 568 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 596 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 564 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.319A pdb=" N TYR A 686 " --> pdb=" O GLY A 962 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 776 through 780 removed outlier: 6.446A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 720 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU A 803 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N CYS A 722 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR A 880 " --> pdb=" O PHE A 915 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 975 through 981 removed outlier: 4.231A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 141 Processing sheet with id=AA8, first strand: chain 'B' and resid 398 through 401 removed outlier: 8.749A pdb=" N GLU B 399 " --> pdb=" O VAL B 373 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 375 " --> pdb=" O GLU B 399 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N TYR B 401 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE B 377 " --> pdb=" O TYR B 401 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N CYS B 422 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLN B 459 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE B 424 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR B 458 " --> pdb=" O ILE B 484 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 535 through 540 removed outlier: 6.869A pdb=" N LEU B 594 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE B 568 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N PHE B 596 " --> pdb=" O ILE B 566 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 564 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 686 through 687 removed outlier: 4.317A pdb=" N TYR B 686 " --> pdb=" O GLY B 962 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 776 through 780 removed outlier: 6.448A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL B 720 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU B 803 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N CYS B 722 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR B 880 " --> pdb=" O PHE B 915 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 975 through 981 removed outlier: 4.191A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 139 through 141 Processing sheet with id=AB5, first strand: chain 'C' and resid 398 through 401 removed outlier: 8.751A pdb=" N GLU C 399 " --> pdb=" O VAL C 373 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE C 375 " --> pdb=" O GLU C 399 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N TYR C 401 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE C 377 " --> pdb=" O TYR C 401 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.523A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR C 458 " --> pdb=" O ILE C 484 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 535 through 540 removed outlier: 6.875A pdb=" N LEU C 594 " --> pdb=" O ILE C 568 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE C 568 " --> pdb=" O LEU C 594 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE C 596 " --> pdb=" O ILE C 566 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU C 564 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.319A pdb=" N TYR C 686 " --> pdb=" O GLY C 962 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 776 through 780 removed outlier: 6.445A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C 720 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU C 803 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N CYS C 722 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N THR C 880 " --> pdb=" O PHE C 915 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 975 through 981 removed outlier: 4.221A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 139 through 141 Processing sheet with id=AC2, first strand: chain 'D' and resid 398 through 401 removed outlier: 8.660A pdb=" N GLU D 399 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ILE D 375 " --> pdb=" O GLU D 399 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N TYR D 401 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE D 377 " --> pdb=" O TYR D 401 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N HIS D 344 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS D 422 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLN D 459 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE D 424 " --> pdb=" O GLN D 459 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR D 458 " --> pdb=" O ILE D 484 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 535 through 540 removed outlier: 6.875A pdb=" N LEU D 594 " --> pdb=" O ILE D 568 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ILE D 568 " --> pdb=" O LEU D 594 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE D 596 " --> pdb=" O ILE D 566 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 564 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 686 through 687 removed outlier: 4.327A pdb=" N TYR D 686 " --> pdb=" O GLY D 962 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 776 through 780 removed outlier: 6.446A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL D 720 " --> pdb=" O VAL D 801 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N LEU D 803 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N CYS D 722 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR D 880 " --> pdb=" O PHE D 915 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 975 through 981 removed outlier: 4.190A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1476 hydrogen bonds defined for protein. 4074 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: 11.54 Time building geometry restraints manager: 8.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9286 1.34 - 1.46: 6479 1.46 - 1.58: 14019 1.58 - 1.69: 0 1.69 - 1.81: 284 Bond restraints: 30068 Sorted by residual: bond pdb=" C PRO A 191 " pdb=" N PRO A 192 " ideal model delta sigma weight residual 1.335 1.350 -0.014 1.36e-02 5.41e+03 1.09e+00 bond pdb=" CA VAL D 190 " pdb=" C VAL D 190 " ideal model delta sigma weight residual 1.524 1.535 -0.011 1.05e-02 9.07e+03 1.06e+00 bond pdb=" C PRO C 191 " pdb=" N PRO C 192 " ideal model delta sigma weight residual 1.335 1.349 -0.014 1.36e-02 5.41e+03 9.97e-01 bond pdb=" C PRO B 191 " pdb=" N PRO B 192 " ideal model delta sigma weight residual 1.335 1.349 -0.013 1.36e-02 5.41e+03 9.77e-01 bond pdb=" C PRO D 191 " pdb=" N PRO D 192 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.36e-02 5.41e+03 9.08e-01 ... (remaining 30063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 39996 1.43 - 2.85: 648 2.85 - 4.28: 110 4.28 - 5.71: 46 5.71 - 7.13: 12 Bond angle restraints: 40812 Sorted by residual: angle pdb=" C TYR C1015 " pdb=" CA TYR C1015 " pdb=" CB TYR C1015 " ideal model delta sigma weight residual 110.62 114.17 -3.55 1.51e+00 4.39e-01 5.53e+00 angle pdb=" C TYR D1015 " pdb=" CA TYR D1015 " pdb=" CB TYR D1015 " ideal model delta sigma weight residual 110.62 114.12 -3.50 1.51e+00 4.39e-01 5.37e+00 angle pdb=" CA ARG C 167 " pdb=" CB ARG C 167 " pdb=" CG ARG C 167 " ideal model delta sigma weight residual 114.10 118.66 -4.56 2.00e+00 2.50e-01 5.20e+00 angle pdb=" CA ARG B 167 " pdb=" CB ARG B 167 " pdb=" CG ARG B 167 " ideal model delta sigma weight residual 114.10 118.55 -4.45 2.00e+00 2.50e-01 4.94e+00 angle pdb=" CA ARG D 167 " pdb=" CB ARG D 167 " pdb=" CG ARG D 167 " ideal model delta sigma weight residual 114.10 118.48 -4.38 2.00e+00 2.50e-01 4.79e+00 ... (remaining 40807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 16849 17.65 - 35.30: 756 35.30 - 52.95: 99 52.95 - 70.60: 12 70.60 - 88.25: 8 Dihedral angle restraints: 17724 sinusoidal: 6892 harmonic: 10832 Sorted by residual: dihedral pdb=" CA TYR C1015 " pdb=" C TYR C1015 " pdb=" N ARG C1016 " pdb=" CA ARG C1016 " ideal model delta harmonic sigma weight residual -180.00 -160.17 -19.83 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR D1015 " pdb=" C TYR D1015 " pdb=" N ARG D1016 " pdb=" CA ARG D1016 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA TYR B1015 " pdb=" C TYR B1015 " pdb=" N ARG B1016 " pdb=" CA ARG B1016 " ideal model delta harmonic sigma weight residual -180.00 -160.58 -19.42 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 17721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 3160 0.036 - 0.072: 1150 0.072 - 0.109: 301 0.109 - 0.145: 80 0.145 - 0.181: 9 Chirality restraints: 4700 Sorted by residual: chirality pdb=" CB VAL A 792 " pdb=" CA VAL A 792 " pdb=" CG1 VAL A 792 " pdb=" CG2 VAL A 792 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CB VAL B 792 " pdb=" CA VAL B 792 " pdb=" CG1 VAL B 792 " pdb=" CG2 VAL B 792 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" CB VAL C 792 " pdb=" CA VAL C 792 " pdb=" CG1 VAL C 792 " pdb=" CG2 VAL C 792 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.92e-01 ... (remaining 4697 not shown) Planarity restraints: 5116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 191 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO A 192 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 192 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 192 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C1015 " -0.015 2.00e-02 2.50e+03 1.37e-02 3.76e+00 pdb=" CG TYR C1015 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C1015 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C1015 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR C1015 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR C1015 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C1015 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C1015 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D1015 " 0.015 2.00e-02 2.50e+03 1.35e-02 3.63e+00 pdb=" CG TYR D1015 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR D1015 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR D1015 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D1015 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D1015 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR D1015 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D1015 " -0.000 2.00e-02 2.50e+03 ... (remaining 5113 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 9951 2.85 - 3.42: 32083 3.42 - 4.00: 54101 4.00 - 4.57: 77186 4.57 - 5.14: 111931 Nonbonded interactions: 285252 Sorted by model distance: nonbonded pdb=" OG1 THR B 284 " pdb=" OH TYR C 290 " model vdw 2.280 3.040 nonbonded pdb=" OG1 THR A 284 " pdb=" OH TYR B 290 " model vdw 2.281 3.040 nonbonded pdb=" OG1 THR C 284 " pdb=" OH TYR D 290 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR A 290 " pdb=" OG1 THR D 284 " model vdw 2.284 3.040 nonbonded pdb=" O VAL A 185 " pdb=" OG1 THR A 189 " model vdw 2.310 3.040 ... (remaining 285247 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: 0.22 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.160 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 65.130 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 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 : 0.002 0.039 30068 Z= 0.115 Angle : 0.502 7.133 40812 Z= 0.263 Chirality : 0.042 0.181 4700 Planarity : 0.004 0.059 5116 Dihedral : 10.165 88.251 10708 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.00 % Allowed : 0.03 % Favored : 99.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.14), residues: 3664 helix: 0.80 (0.12), residues: 1880 sheet: 0.39 (0.25), residues: 456 loop : 0.22 (0.16), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 23 HIS 0.002 0.001 HIS C 718 PHE 0.032 0.002 PHE D 194 TYR 0.034 0.001 TYR C1015 ARG 0.003 0.000 ARG A 113 Details of bonding type rmsd hydrogen bonds : bond 0.14953 ( 1476) hydrogen bonds : angle 5.38269 ( 4074) covalent geometry : bond 0.00244 (30068) covalent geometry : angle 0.50170 (40812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 354 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 TRP cc_start: 0.7741 (p90) cc_final: 0.6887 (t60) REVERT: A 372 ASN cc_start: 0.7127 (t0) cc_final: 0.6668 (t0) REVERT: B 23 TRP cc_start: 0.7725 (p90) cc_final: 0.6880 (t60) REVERT: B 157 ASN cc_start: 0.8636 (m110) cc_final: 0.8338 (t0) REVERT: B 159 PHE cc_start: 0.8287 (t80) cc_final: 0.7874 (t80) REVERT: B 198 TYR cc_start: 0.8544 (t80) cc_final: 0.8318 (t80) REVERT: B 372 ASN cc_start: 0.7211 (t0) cc_final: 0.6764 (t0) REVERT: C 372 ASN cc_start: 0.7209 (t0) cc_final: 0.6754 (t0) REVERT: D 23 TRP cc_start: 0.7714 (p90) cc_final: 0.6928 (t60) REVERT: D 159 PHE cc_start: 0.8285 (t80) cc_final: 0.7928 (t80) REVERT: D 372 ASN cc_start: 0.7113 (t0) cc_final: 0.6665 (t0) REVERT: E 260 ARG cc_start: 0.5468 (mtt180) cc_final: 0.4556 (mmt180) REVERT: F 260 ARG cc_start: 0.5927 (mtt180) cc_final: 0.4863 (tpt90) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 1.2770 time to fit residues: 536.5867 Evaluate side-chains 232 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 3.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 188 optimal weight: 0.0010 chunk 149 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 214 optimal weight: 2.9990 chunk 334 optimal weight: 0.5980 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.087965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.058048 restraints weight = 73372.999| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.40 r_work: 0.2795 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 30068 Z= 0.110 Angle : 0.516 11.748 40812 Z= 0.260 Chirality : 0.040 0.191 4700 Planarity : 0.004 0.039 5116 Dihedral : 3.560 17.360 3964 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.42 % Allowed : 6.40 % Favored : 92.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.14), residues: 3664 helix: 1.18 (0.12), residues: 1876 sheet: 0.57 (0.26), residues: 452 loop : 0.72 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 23 HIS 0.002 0.000 HIS B 394 PHE 0.020 0.001 PHE A 144 TYR 0.022 0.001 TYR C1015 ARG 0.005 0.000 ARG C 329 Details of bonding type rmsd hydrogen bonds : bond 0.04219 ( 1476) hydrogen bonds : angle 4.37071 ( 4074) covalent geometry : bond 0.00238 (30068) covalent geometry : angle 0.51597 (40812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9276 (mmm) cc_final: 0.8915 (ptm) REVERT: A 154 MET cc_start: 0.8318 (tpp) cc_final: 0.7938 (tpt) REVERT: A 159 PHE cc_start: 0.7850 (t80) cc_final: 0.7648 (t80) REVERT: A 372 ASN cc_start: 0.6945 (t0) cc_final: 0.6440 (t0) REVERT: A 806 ASN cc_start: 0.8592 (t0) cc_final: 0.8295 (m-40) REVERT: B 154 MET cc_start: 0.8343 (tpp) cc_final: 0.7967 (tpp) REVERT: B 159 PHE cc_start: 0.8190 (t80) cc_final: 0.7896 (t80) REVERT: B 198 TYR cc_start: 0.8576 (t80) cc_final: 0.8110 (t80) REVERT: B 372 ASN cc_start: 0.7026 (t0) cc_final: 0.6528 (t0) REVERT: B 574 ASN cc_start: 0.8429 (OUTLIER) cc_final: 0.7854 (p0) REVERT: B 806 ASN cc_start: 0.8549 (t0) cc_final: 0.8340 (m-40) REVERT: C 30 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.8969 (ptt) REVERT: C 154 MET cc_start: 0.8557 (tpp) cc_final: 0.8086 (tpp) REVERT: C 159 PHE cc_start: 0.8443 (t80) cc_final: 0.8137 (t80) REVERT: C 372 ASN cc_start: 0.7028 (t0) cc_final: 0.6523 (t0) REVERT: C 574 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.7853 (p0) REVERT: C 806 ASN cc_start: 0.8550 (t0) cc_final: 0.8342 (m-40) REVERT: D 30 MET cc_start: 0.9307 (mmm) cc_final: 0.8799 (ptt) REVERT: D 154 MET cc_start: 0.8514 (tpp) cc_final: 0.8095 (tpp) REVERT: D 159 PHE cc_start: 0.8229 (t80) cc_final: 0.7970 (t80) REVERT: D 372 ASN cc_start: 0.6936 (t0) cc_final: 0.6447 (t0) REVERT: D 806 ASN cc_start: 0.8578 (t0) cc_final: 0.8310 (m-40) REVERT: E 260 ARG cc_start: 0.5807 (mtt180) cc_final: 0.4641 (tpt90) REVERT: E 262 LEU cc_start: 0.8995 (mt) cc_final: 0.8786 (tt) REVERT: E 266 TYR cc_start: 0.8482 (m-10) cc_final: 0.8200 (m-80) REVERT: E 268 LEU cc_start: 0.9032 (tt) cc_final: 0.8696 (tt) REVERT: F 260 ARG cc_start: 0.5561 (mtt180) cc_final: 0.4170 (tpt90) REVERT: F 266 TYR cc_start: 0.8574 (m-10) cc_final: 0.8361 (m-80) REVERT: G 266 TYR cc_start: 0.8108 (m-10) cc_final: 0.7708 (m-80) REVERT: H 259 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6146 (mp) outliers start: 46 outliers final: 13 residues processed: 271 average time/residue: 1.1375 time to fit residues: 379.2714 Evaluate side-chains 250 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain H residue 259 LEU Chi-restraints excluded: chain H residue 261 ASP Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 181 optimal weight: 6.9990 chunk 305 optimal weight: 0.4980 chunk 242 optimal weight: 1.9990 chunk 279 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 315 optimal weight: 2.9990 chunk 217 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 351 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 254 HIS ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 HIS ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.086840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.056826 restraints weight = 73640.721| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.39 r_work: 0.2767 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30068 Z= 0.140 Angle : 0.513 12.652 40812 Z= 0.257 Chirality : 0.040 0.146 4700 Planarity : 0.003 0.034 5116 Dihedral : 3.467 16.008 3964 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.14 % Allowed : 8.13 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.14), residues: 3664 helix: 1.29 (0.12), residues: 1876 sheet: 0.65 (0.26), residues: 452 loop : 0.77 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 275 HIS 0.002 0.001 HIS B 468 PHE 0.016 0.001 PHE A 511 TYR 0.020 0.001 TYR C1015 ARG 0.003 0.000 ARG D 329 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 1476) hydrogen bonds : angle 4.28082 ( 4074) covalent geometry : bond 0.00328 (30068) covalent geometry : angle 0.51342 (40812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 239 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9256 (mmm) cc_final: 0.8863 (ptm) REVERT: A 372 ASN cc_start: 0.6918 (t0) cc_final: 0.6372 (t0) REVERT: A 739 MET cc_start: 0.9462 (mtm) cc_final: 0.9214 (mtp) REVERT: A 806 ASN cc_start: 0.8624 (t0) cc_final: 0.8409 (m-40) REVERT: B 30 MET cc_start: 0.9340 (mmm) cc_final: 0.8833 (ptt) REVERT: B 154 MET cc_start: 0.8501 (tpp) cc_final: 0.7999 (tpt) REVERT: B 198 TYR cc_start: 0.8768 (t80) cc_final: 0.8511 (t80) REVERT: B 372 ASN cc_start: 0.6956 (t0) cc_final: 0.6466 (t0) REVERT: B 574 ASN cc_start: 0.8450 (OUTLIER) cc_final: 0.7878 (p0) REVERT: B 739 MET cc_start: 0.9454 (mtm) cc_final: 0.9202 (mtp) REVERT: B 806 ASN cc_start: 0.8613 (t0) cc_final: 0.8406 (m-40) REVERT: C 30 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.8931 (ptm) REVERT: C 154 MET cc_start: 0.8741 (tpp) cc_final: 0.8280 (tpt) REVERT: C 159 PHE cc_start: 0.8376 (t80) cc_final: 0.7974 (t80) REVERT: C 372 ASN cc_start: 0.6955 (t0) cc_final: 0.6464 (t0) REVERT: C 574 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.7933 (p0) REVERT: C 739 MET cc_start: 0.9456 (mtm) cc_final: 0.9205 (mtp) REVERT: C 806 ASN cc_start: 0.8612 (t0) cc_final: 0.8407 (m-40) REVERT: D 154 MET cc_start: 0.8589 (tpp) cc_final: 0.8271 (tpp) REVERT: D 198 TYR cc_start: 0.8716 (t80) cc_final: 0.8183 (t80) REVERT: D 372 ASN cc_start: 0.6869 (t0) cc_final: 0.6377 (t0) REVERT: D 739 MET cc_start: 0.9468 (mtm) cc_final: 0.9222 (mtp) REVERT: E 260 ARG cc_start: 0.5820 (mtt180) cc_final: 0.4645 (mmt180) REVERT: E 262 LEU cc_start: 0.9019 (mt) cc_final: 0.8778 (tt) REVERT: E 266 TYR cc_start: 0.8526 (m-10) cc_final: 0.8171 (m-80) REVERT: F 260 ARG cc_start: 0.5528 (mtt180) cc_final: 0.4008 (mtp180) REVERT: G 266 TYR cc_start: 0.8200 (m-10) cc_final: 0.7968 (m-80) outliers start: 37 outliers final: 20 residues processed: 255 average time/residue: 1.0611 time to fit residues: 333.1565 Evaluate side-chains 256 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 30 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 259 LEU Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 261 ASP Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 196 optimal weight: 6.9990 chunk 346 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 327 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 173 optimal weight: 9.9990 chunk 99 optimal weight: 20.0000 chunk 111 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 chunk 28 optimal weight: 0.3980 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.085406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.055358 restraints weight = 74179.380| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.37 r_work: 0.2729 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 30068 Z= 0.187 Angle : 0.539 12.502 40812 Z= 0.268 Chirality : 0.042 0.151 4700 Planarity : 0.003 0.033 5116 Dihedral : 3.524 15.178 3964 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.33 % Allowed : 8.71 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.14), residues: 3664 helix: 1.27 (0.12), residues: 1888 sheet: 0.65 (0.26), residues: 452 loop : 0.65 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 275 HIS 0.003 0.001 HIS B 468 PHE 0.024 0.001 PHE D 159 TYR 0.023 0.001 TYR F 266 ARG 0.003 0.000 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.04378 ( 1476) hydrogen bonds : angle 4.28382 ( 4074) covalent geometry : bond 0.00446 (30068) covalent geometry : angle 0.53939 (40812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 3.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9351 (mmm) cc_final: 0.8833 (ptt) REVERT: A 154 MET cc_start: 0.8676 (tpp) cc_final: 0.8173 (tpp) REVERT: A 194 PHE cc_start: 0.9318 (m-10) cc_final: 0.9101 (m-10) REVERT: A 372 ASN cc_start: 0.6838 (t0) cc_final: 0.6367 (t0) REVERT: A 739 MET cc_start: 0.9485 (mtm) cc_final: 0.9248 (mtp) REVERT: A 806 ASN cc_start: 0.8713 (t0) cc_final: 0.8481 (m-40) REVERT: B 21 MET cc_start: 0.8782 (tpp) cc_final: 0.8557 (tpp) REVERT: B 153 ASP cc_start: 0.8478 (t0) cc_final: 0.8265 (t0) REVERT: B 154 MET cc_start: 0.8685 (tpp) cc_final: 0.8323 (tpp) REVERT: B 198 TYR cc_start: 0.8859 (t80) cc_final: 0.8484 (t80) REVERT: B 372 ASN cc_start: 0.6966 (t0) cc_final: 0.6432 (t0) REVERT: B 574 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.7905 (p0) REVERT: B 739 MET cc_start: 0.9486 (mtm) cc_final: 0.9249 (mtp) REVERT: B 806 ASN cc_start: 0.8709 (t0) cc_final: 0.8481 (m-40) REVERT: C 34 PHE cc_start: 0.9336 (m-10) cc_final: 0.9130 (m-10) REVERT: C 154 MET cc_start: 0.8895 (tpp) cc_final: 0.8614 (tpp) REVERT: C 372 ASN cc_start: 0.6968 (t0) cc_final: 0.6426 (t0) REVERT: C 574 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.7867 (p0) REVERT: C 739 MET cc_start: 0.9488 (mtm) cc_final: 0.9254 (mtp) REVERT: C 806 ASN cc_start: 0.8705 (t0) cc_final: 0.8495 (m-40) REVERT: C 807 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: D 21 MET cc_start: 0.8733 (tpp) cc_final: 0.8514 (tpp) REVERT: D 154 MET cc_start: 0.8806 (tpp) cc_final: 0.8403 (tpp) REVERT: D 198 TYR cc_start: 0.8816 (t80) cc_final: 0.8435 (t80) REVERT: D 372 ASN cc_start: 0.6828 (t0) cc_final: 0.6357 (t0) REVERT: D 739 MET cc_start: 0.9489 (mtm) cc_final: 0.9255 (mtp) REVERT: E 260 ARG cc_start: 0.5812 (mtt180) cc_final: 0.4962 (ttt180) REVERT: E 262 LEU cc_start: 0.8998 (mt) cc_final: 0.8782 (tt) REVERT: E 266 TYR cc_start: 0.8563 (m-10) cc_final: 0.8229 (m-80) REVERT: F 260 ARG cc_start: 0.5147 (mtt180) cc_final: 0.3659 (mtp180) REVERT: F 262 LEU cc_start: 0.8964 (pp) cc_final: 0.8697 (pp) REVERT: F 266 TYR cc_start: 0.8457 (m-10) cc_final: 0.8204 (m-80) REVERT: G 266 TYR cc_start: 0.8278 (m-10) cc_final: 0.7991 (m-80) REVERT: H 262 LEU cc_start: 0.8643 (pp) cc_final: 0.8394 (pp) outliers start: 43 outliers final: 22 residues processed: 267 average time/residue: 1.0779 time to fit residues: 354.0285 Evaluate side-chains 254 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain C residue 807 GLN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 279 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 180 optimal weight: 30.0000 chunk 133 optimal weight: 0.9980 chunk 327 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 247 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 chunk 337 optimal weight: 0.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.085960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.056725 restraints weight = 72763.728| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.32 r_work: 0.2757 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30068 Z= 0.119 Angle : 0.513 10.897 40812 Z= 0.252 Chirality : 0.040 0.143 4700 Planarity : 0.003 0.037 5116 Dihedral : 3.461 13.936 3964 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.02 % Allowed : 9.70 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.14), residues: 3664 helix: 1.38 (0.12), residues: 1884 sheet: 0.70 (0.26), residues: 452 loop : 0.67 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 275 HIS 0.002 0.001 HIS B 468 PHE 0.028 0.001 PHE D 159 TYR 0.023 0.001 TYR H 266 ARG 0.002 0.000 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 1476) hydrogen bonds : angle 4.16132 ( 4074) covalent geometry : bond 0.00274 (30068) covalent geometry : angle 0.51288 (40812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9391 (mmm) cc_final: 0.8872 (ptt) REVERT: A 372 ASN cc_start: 0.6723 (t0) cc_final: 0.6229 (t0) REVERT: A 806 ASN cc_start: 0.8693 (t0) cc_final: 0.8473 (m-40) REVERT: B 153 ASP cc_start: 0.8442 (t0) cc_final: 0.8214 (t0) REVERT: B 154 MET cc_start: 0.8635 (tpp) cc_final: 0.8327 (tpp) REVERT: B 198 TYR cc_start: 0.8898 (t80) cc_final: 0.8509 (t80) REVERT: B 372 ASN cc_start: 0.6892 (t0) cc_final: 0.6199 (t0) REVERT: B 574 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.7957 (p0) REVERT: B 806 ASN cc_start: 0.8672 (t0) cc_final: 0.8445 (m-40) REVERT: C 30 MET cc_start: 0.9443 (mmm) cc_final: 0.8866 (ptm) REVERT: C 154 MET cc_start: 0.8903 (tpp) cc_final: 0.8477 (tpp) REVERT: C 372 ASN cc_start: 0.6885 (t0) cc_final: 0.6189 (t0) REVERT: C 574 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.7930 (p0) REVERT: C 806 ASN cc_start: 0.8695 (t0) cc_final: 0.8472 (m-40) REVERT: D 21 MET cc_start: 0.8817 (tpp) cc_final: 0.8587 (tpp) REVERT: D 154 MET cc_start: 0.8743 (tpp) cc_final: 0.8535 (tpp) REVERT: D 198 TYR cc_start: 0.8811 (t80) cc_final: 0.8377 (t80) REVERT: D 372 ASN cc_start: 0.6718 (t0) cc_final: 0.6240 (t0) REVERT: E 260 ARG cc_start: 0.5775 (mtt180) cc_final: 0.5003 (ttt180) REVERT: E 262 LEU cc_start: 0.9024 (mt) cc_final: 0.8755 (tt) REVERT: E 266 TYR cc_start: 0.8548 (m-10) cc_final: 0.8184 (m-80) REVERT: F 260 ARG cc_start: 0.5101 (mtt180) cc_final: 0.3740 (mtp180) REVERT: F 262 LEU cc_start: 0.8919 (pp) cc_final: 0.8715 (pp) REVERT: G 266 TYR cc_start: 0.8231 (m-10) cc_final: 0.7960 (m-80) REVERT: H 262 LEU cc_start: 0.8622 (pp) cc_final: 0.8395 (pp) REVERT: H 266 TYR cc_start: 0.8049 (m-10) cc_final: 0.7815 (m-80) outliers start: 33 outliers final: 17 residues processed: 253 average time/residue: 1.0714 time to fit residues: 332.9446 Evaluate side-chains 243 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 224 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain G residue 279 SER Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 320 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 278 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 221 optimal weight: 1.9990 chunk 243 optimal weight: 2.9990 chunk 131 optimal weight: 0.2980 chunk 46 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.086599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.056625 restraints weight = 73859.274| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.39 r_work: 0.2762 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30068 Z= 0.115 Angle : 0.513 11.132 40812 Z= 0.251 Chirality : 0.040 0.141 4700 Planarity : 0.003 0.037 5116 Dihedral : 3.414 13.541 3964 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.96 % Allowed : 9.92 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.14), residues: 3664 helix: 1.43 (0.12), residues: 1884 sheet: 0.75 (0.26), residues: 452 loop : 0.77 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 275 HIS 0.002 0.001 HIS A 254 PHE 0.031 0.001 PHE D 159 TYR 0.022 0.001 TYR F 266 ARG 0.002 0.000 ARG B 329 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 1476) hydrogen bonds : angle 4.06196 ( 4074) covalent geometry : bond 0.00265 (30068) covalent geometry : angle 0.51259 (40812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 3.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9434 (mmm) cc_final: 0.8924 (ptm) REVERT: A 372 ASN cc_start: 0.6705 (t0) cc_final: 0.6087 (t0) REVERT: A 806 ASN cc_start: 0.8700 (t0) cc_final: 0.8459 (t0) REVERT: B 21 MET cc_start: 0.8680 (tpp) cc_final: 0.8469 (tpp) REVERT: B 153 ASP cc_start: 0.8477 (t0) cc_final: 0.8238 (t0) REVERT: B 154 MET cc_start: 0.8631 (tpp) cc_final: 0.8368 (tpp) REVERT: B 198 TYR cc_start: 0.8930 (t80) cc_final: 0.8563 (t80) REVERT: B 252 PHE cc_start: 0.8528 (OUTLIER) cc_final: 0.8177 (t80) REVERT: B 372 ASN cc_start: 0.6835 (t0) cc_final: 0.6179 (t0) REVERT: B 574 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.7989 (p0) REVERT: B 806 ASN cc_start: 0.8703 (t0) cc_final: 0.8461 (t0) REVERT: C 30 MET cc_start: 0.9401 (mmm) cc_final: 0.8915 (ptm) REVERT: C 372 ASN cc_start: 0.6877 (t0) cc_final: 0.6225 (t0) REVERT: C 574 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8012 (p0) REVERT: C 806 ASN cc_start: 0.8715 (t0) cc_final: 0.8451 (t0) REVERT: D 21 MET cc_start: 0.8864 (tpp) cc_final: 0.8653 (tpp) REVERT: D 198 TYR cc_start: 0.8733 (t80) cc_final: 0.8350 (t80) REVERT: D 252 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8180 (t80) REVERT: D 372 ASN cc_start: 0.6701 (t0) cc_final: 0.6087 (t0) REVERT: E 260 ARG cc_start: 0.5746 (mtt180) cc_final: 0.4990 (ttt180) REVERT: E 262 LEU cc_start: 0.9046 (mt) cc_final: 0.8773 (tt) REVERT: E 266 TYR cc_start: 0.8579 (m-10) cc_final: 0.8229 (m-80) REVERT: F 260 ARG cc_start: 0.4764 (mtt180) cc_final: 0.3389 (mtp180) REVERT: F 266 TYR cc_start: 0.8291 (m-10) cc_final: 0.8039 (m-80) REVERT: G 266 TYR cc_start: 0.8255 (m-10) cc_final: 0.8010 (m-80) REVERT: H 262 LEU cc_start: 0.8696 (pp) cc_final: 0.8391 (pp) REVERT: H 266 TYR cc_start: 0.8093 (m-10) cc_final: 0.7866 (m-10) outliers start: 31 outliers final: 14 residues processed: 257 average time/residue: 1.1032 time to fit residues: 354.3589 Evaluate side-chains 247 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 229 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 574 ASN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain F residue 279 SER Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 10 optimal weight: 3.9990 chunk 274 optimal weight: 7.9990 chunk 293 optimal weight: 0.3980 chunk 340 optimal weight: 0.0040 chunk 328 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 354 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 262 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 overall best weight: 1.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 ASN ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.086488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056506 restraints weight = 73676.935| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 3.38 r_work: 0.2760 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30068 Z= 0.123 Angle : 0.525 13.101 40812 Z= 0.255 Chirality : 0.040 0.149 4700 Planarity : 0.003 0.037 5116 Dihedral : 3.404 13.506 3964 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.96 % Allowed : 10.14 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.14), residues: 3664 helix: 1.42 (0.12), residues: 1888 sheet: 0.72 (0.25), residues: 452 loop : 0.77 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 275 HIS 0.002 0.001 HIS B 254 PHE 0.031 0.001 PHE D 159 TYR 0.012 0.001 TYR A1015 ARG 0.002 0.000 ARG D 329 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 1476) hydrogen bonds : angle 4.05733 ( 4074) covalent geometry : bond 0.00286 (30068) covalent geometry : angle 0.52510 (40812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 3.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9414 (mmm) cc_final: 0.8915 (ptm) REVERT: A 154 MET cc_start: 0.9016 (tpt) cc_final: 0.8690 (tpp) REVERT: A 252 PHE cc_start: 0.8489 (OUTLIER) cc_final: 0.8128 (t80) REVERT: A 372 ASN cc_start: 0.6695 (t0) cc_final: 0.6062 (t0) REVERT: A 806 ASN cc_start: 0.8712 (t0) cc_final: 0.8447 (t0) REVERT: B 153 ASP cc_start: 0.8491 (t0) cc_final: 0.8256 (t0) REVERT: B 198 TYR cc_start: 0.9000 (t80) cc_final: 0.8502 (t80) REVERT: B 252 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8160 (t80) REVERT: B 372 ASN cc_start: 0.6863 (t0) cc_final: 0.6216 (t0) REVERT: B 574 ASN cc_start: 0.8606 (OUTLIER) cc_final: 0.8037 (p0) REVERT: B 806 ASN cc_start: 0.8726 (t0) cc_final: 0.8478 (t0) REVERT: C 30 MET cc_start: 0.9375 (mmm) cc_final: 0.8906 (ptm) REVERT: C 198 TYR cc_start: 0.8797 (t80) cc_final: 0.8393 (t80) REVERT: C 372 ASN cc_start: 0.6860 (t0) cc_final: 0.6218 (t0) REVERT: C 806 ASN cc_start: 0.8723 (t0) cc_final: 0.8475 (t0) REVERT: D 21 MET cc_start: 0.8894 (tpp) cc_final: 0.8667 (tpp) REVERT: D 154 MET cc_start: 0.8686 (tpp) cc_final: 0.8194 (tpp) REVERT: D 198 TYR cc_start: 0.8739 (t80) cc_final: 0.8334 (t80) REVERT: D 252 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.8167 (t80) REVERT: D 372 ASN cc_start: 0.6702 (t0) cc_final: 0.6067 (t0) REVERT: E 260 ARG cc_start: 0.5774 (mtt180) cc_final: 0.4953 (ttt180) REVERT: E 262 LEU cc_start: 0.9023 (mt) cc_final: 0.8765 (tt) REVERT: E 266 TYR cc_start: 0.8528 (m-10) cc_final: 0.8183 (m-80) REVERT: F 260 ARG cc_start: 0.4244 (mtt180) cc_final: 0.3057 (mtp180) REVERT: F 262 LEU cc_start: 0.8969 (pp) cc_final: 0.8676 (pt) REVERT: G 266 TYR cc_start: 0.8263 (m-10) cc_final: 0.8016 (m-80) REVERT: H 262 LEU cc_start: 0.8723 (pp) cc_final: 0.8374 (pp) outliers start: 31 outliers final: 14 residues processed: 250 average time/residue: 1.0872 time to fit residues: 334.5298 Evaluate side-chains 242 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 224 time to evaluate : 3.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain H residue 272 SER Chi-restraints excluded: chain H residue 279 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 156 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 186 optimal weight: 8.9990 chunk 365 optimal weight: 0.3980 chunk 208 optimal weight: 7.9990 chunk 255 optimal weight: 0.0470 chunk 176 optimal weight: 10.0000 chunk 300 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 140 optimal weight: 7.9990 overall best weight: 1.6482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.086698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.056713 restraints weight = 73914.358| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.39 r_work: 0.2767 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30068 Z= 0.117 Angle : 0.534 11.973 40812 Z= 0.258 Chirality : 0.040 0.149 4700 Planarity : 0.003 0.037 5116 Dihedral : 3.402 13.377 3964 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.87 % Allowed : 10.38 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.14), residues: 3664 helix: 1.44 (0.12), residues: 1884 sheet: 0.75 (0.25), residues: 452 loop : 0.79 (0.17), residues: 1328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 275 HIS 0.002 0.001 HIS A 254 PHE 0.033 0.001 PHE C 144 TYR 0.024 0.001 TYR F 266 ARG 0.002 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 1476) hydrogen bonds : angle 4.03925 ( 4074) covalent geometry : bond 0.00270 (30068) covalent geometry : angle 0.53417 (40812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9437 (mmm) cc_final: 0.8910 (ptm) REVERT: A 154 MET cc_start: 0.9024 (tpt) cc_final: 0.8678 (tpp) REVERT: A 252 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.8155 (t80) REVERT: A 372 ASN cc_start: 0.6719 (t0) cc_final: 0.6096 (t0) REVERT: A 806 ASN cc_start: 0.8691 (t0) cc_final: 0.8416 (t0) REVERT: B 154 MET cc_start: 0.8860 (tpt) cc_final: 0.8346 (tpp) REVERT: B 198 TYR cc_start: 0.8943 (t80) cc_final: 0.8571 (t80) REVERT: B 252 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8188 (t80) REVERT: B 372 ASN cc_start: 0.6871 (t0) cc_final: 0.6231 (t0) REVERT: B 574 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8023 (p0) REVERT: B 806 ASN cc_start: 0.8713 (t0) cc_final: 0.8453 (t0) REVERT: C 30 MET cc_start: 0.9368 (mmm) cc_final: 0.8908 (ptm) REVERT: C 154 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8845 (tpp) REVERT: C 252 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8173 (t80) REVERT: C 372 ASN cc_start: 0.6885 (t0) cc_final: 0.6214 (t0) REVERT: C 806 ASN cc_start: 0.8705 (t0) cc_final: 0.8446 (t0) REVERT: D 21 MET cc_start: 0.8872 (tpp) cc_final: 0.8637 (tpp) REVERT: D 154 MET cc_start: 0.8728 (tpp) cc_final: 0.8209 (tpp) REVERT: D 198 TYR cc_start: 0.8746 (t80) cc_final: 0.8322 (t80) REVERT: D 252 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8192 (t80) REVERT: D 372 ASN cc_start: 0.6688 (t0) cc_final: 0.5981 (t0) REVERT: E 260 ARG cc_start: 0.5774 (mtt180) cc_final: 0.4936 (ttt180) REVERT: E 262 LEU cc_start: 0.9026 (mt) cc_final: 0.8758 (tt) REVERT: E 266 TYR cc_start: 0.8591 (m-10) cc_final: 0.8229 (m-80) REVERT: F 260 ARG cc_start: 0.4462 (mtt180) cc_final: 0.2969 (mtp180) REVERT: G 266 TYR cc_start: 0.8236 (m-10) cc_final: 0.8008 (m-80) outliers start: 28 outliers final: 11 residues processed: 249 average time/residue: 1.0559 time to fit residues: 323.2242 Evaluate side-chains 241 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain H residue 272 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 337 optimal weight: 0.5980 chunk 171 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 55 optimal weight: 0.0270 chunk 331 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 221 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 overall best weight: 1.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.086973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.057872 restraints weight = 72780.181| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 3.27 r_work: 0.2782 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30068 Z= 0.111 Angle : 0.543 15.265 40812 Z= 0.264 Chirality : 0.040 0.169 4700 Planarity : 0.003 0.037 5116 Dihedral : 3.384 13.240 3964 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 0.87 % Allowed : 10.63 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.14), residues: 3664 helix: 1.41 (0.12), residues: 1888 sheet: 0.79 (0.26), residues: 452 loop : 0.82 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 275 HIS 0.002 0.000 HIS A 254 PHE 0.029 0.001 PHE C 144 TYR 0.020 0.001 TYR F 266 ARG 0.002 0.000 ARG C 329 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 1476) hydrogen bonds : angle 4.02834 ( 4074) covalent geometry : bond 0.00253 (30068) covalent geometry : angle 0.54320 (40812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 3.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9446 (mmm) cc_final: 0.8794 (ptt) REVERT: A 252 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.8188 (t80) REVERT: A 372 ASN cc_start: 0.6706 (t0) cc_final: 0.6014 (t0) REVERT: A 806 ASN cc_start: 0.8681 (t0) cc_final: 0.8416 (t0) REVERT: B 154 MET cc_start: 0.8866 (tpt) cc_final: 0.8520 (tpp) REVERT: B 198 TYR cc_start: 0.8897 (t80) cc_final: 0.8595 (t80) REVERT: B 252 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8189 (t80) REVERT: B 372 ASN cc_start: 0.6849 (t0) cc_final: 0.6218 (t0) REVERT: B 574 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8034 (p0) REVERT: B 806 ASN cc_start: 0.8702 (t0) cc_final: 0.8437 (t0) REVERT: C 30 MET cc_start: 0.9385 (mmm) cc_final: 0.8944 (ptt) REVERT: C 252 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.8203 (t80) REVERT: C 372 ASN cc_start: 0.6860 (t0) cc_final: 0.6229 (t0) REVERT: C 806 ASN cc_start: 0.8689 (t0) cc_final: 0.8439 (t0) REVERT: D 21 MET cc_start: 0.8872 (tpp) cc_final: 0.8671 (tpp) REVERT: D 154 MET cc_start: 0.8744 (tpp) cc_final: 0.8302 (tpp) REVERT: D 198 TYR cc_start: 0.8739 (t80) cc_final: 0.8350 (t80) REVERT: D 252 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8196 (t80) REVERT: D 372 ASN cc_start: 0.6692 (t0) cc_final: 0.5987 (t0) REVERT: E 260 ARG cc_start: 0.5838 (mtt180) cc_final: 0.4593 (mmt180) REVERT: E 262 LEU cc_start: 0.8981 (mt) cc_final: 0.8720 (tt) REVERT: E 266 TYR cc_start: 0.8570 (m-10) cc_final: 0.8201 (m-80) REVERT: F 260 ARG cc_start: 0.4415 (mtt180) cc_final: 0.2891 (mtp180) REVERT: G 266 TYR cc_start: 0.8212 (m-10) cc_final: 0.7978 (m-80) outliers start: 28 outliers final: 15 residues processed: 247 average time/residue: 1.0895 time to fit residues: 330.2758 Evaluate side-chains 243 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 223 time to evaluate : 3.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 574 ASN Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain H residue 272 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 121 optimal weight: 9.9990 chunk 273 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 237 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 ASN ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.085276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.055933 restraints weight = 72722.478| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 3.27 r_work: 0.2731 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 30068 Z= 0.192 Angle : 0.597 13.146 40812 Z= 0.293 Chirality : 0.042 0.186 4700 Planarity : 0.003 0.035 5116 Dihedral : 3.533 14.497 3964 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.05 % Allowed : 10.57 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.14), residues: 3664 helix: 1.26 (0.12), residues: 1896 sheet: 0.65 (0.25), residues: 452 loop : 0.76 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 23 HIS 0.003 0.001 HIS D 468 PHE 0.036 0.001 PHE A 159 TYR 0.014 0.001 TYR C1015 ARG 0.002 0.000 ARG A 790 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 1476) hydrogen bonds : angle 4.21259 ( 4074) covalent geometry : bond 0.00458 (30068) covalent geometry : angle 0.59699 (40812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7328 Ramachandran restraints generated. 3664 Oldfield, 0 Emsley, 3664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.9435 (mmm) cc_final: 0.8841 (ptm) REVERT: A 252 PHE cc_start: 0.8552 (OUTLIER) cc_final: 0.8124 (t80) REVERT: A 372 ASN cc_start: 0.6803 (t0) cc_final: 0.6102 (t0) REVERT: A 806 ASN cc_start: 0.8757 (t0) cc_final: 0.8465 (t0) REVERT: B 198 TYR cc_start: 0.9012 (t80) cc_final: 0.8620 (t80) REVERT: B 252 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.8161 (t80) REVERT: B 372 ASN cc_start: 0.6866 (t0) cc_final: 0.6155 (t0) REVERT: B 806 ASN cc_start: 0.8762 (t0) cc_final: 0.8469 (t0) REVERT: C 30 MET cc_start: 0.9390 (mmm) cc_final: 0.8956 (ptt) REVERT: C 198 TYR cc_start: 0.8936 (t80) cc_final: 0.8571 (t80) REVERT: C 252 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.8161 (t80) REVERT: C 372 ASN cc_start: 0.6872 (t0) cc_final: 0.6164 (t0) REVERT: C 806 ASN cc_start: 0.8750 (t0) cc_final: 0.8459 (t0) REVERT: D 154 MET cc_start: 0.8812 (tpp) cc_final: 0.8353 (tpp) REVERT: D 198 TYR cc_start: 0.8743 (t80) cc_final: 0.8336 (t80) REVERT: D 252 PHE cc_start: 0.8568 (OUTLIER) cc_final: 0.8170 (t80) REVERT: D 372 ASN cc_start: 0.6785 (t0) cc_final: 0.6079 (t0) REVERT: E 260 ARG cc_start: 0.5842 (mtt180) cc_final: 0.4508 (mmt180) REVERT: E 262 LEU cc_start: 0.8936 (mt) cc_final: 0.8692 (tt) REVERT: E 266 TYR cc_start: 0.8578 (m-10) cc_final: 0.8261 (m-80) REVERT: G 266 TYR cc_start: 0.8247 (m-10) cc_final: 0.7965 (m-80) REVERT: H 262 LEU cc_start: 0.8546 (pt) cc_final: 0.8253 (pt) outliers start: 34 outliers final: 20 residues processed: 240 average time/residue: 1.0915 time to fit residues: 320.6961 Evaluate side-chains 240 residues out of total 3236 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 216 time to evaluate : 2.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 941 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 941 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 252 PHE Chi-restraints excluded: chain C residue 460 MET Chi-restraints excluded: chain C residue 941 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 252 PHE Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 941 VAL Chi-restraints excluded: chain E residue 272 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain H residue 272 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 290 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 154 optimal weight: 0.9980 chunk 294 optimal weight: 10.0000 chunk 246 optimal weight: 0.8980 chunk 359 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 247 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.087119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057965 restraints weight = 72534.897| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.27 r_work: 0.2781 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30068 Z= 0.109 Angle : 0.553 11.311 40812 Z= 0.269 Chirality : 0.040 0.189 4700 Planarity : 0.003 0.037 5116 Dihedral : 3.440 15.382 3964 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.96 % Allowed : 10.82 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.14), residues: 3664 helix: 1.38 (0.12), residues: 1892 sheet: 0.76 (0.26), residues: 452 loop : 0.77 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 275 HIS 0.002 0.000 HIS C 254 PHE 0.049 0.001 PHE B 159 TYR 0.012 0.001 TYR H 266 ARG 0.002 0.000 ARG C 329 Details of bonding type rmsd hydrogen bonds : bond 0.03571 ( 1476) hydrogen bonds : angle 4.05378 ( 4074) covalent geometry : bond 0.00246 (30068) covalent geometry : angle 0.55290 (40812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17201.44 seconds wall clock time: 298 minutes 9.46 seconds (17889.46 seconds total)