Starting phenix.real_space_refine on Thu May 29 05:44:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v64_42989/05_2025/8v64_42989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v64_42989/05_2025/8v64_42989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8v64_42989/05_2025/8v64_42989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v64_42989/05_2025/8v64_42989.map" model { file = "/net/cci-nas-00/data/ceres_data/8v64_42989/05_2025/8v64_42989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v64_42989/05_2025/8v64_42989.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.028 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: 6 Type Number sf(0) Gaussians K 9 8.98 5 P 20 5.49 5 S 192 5.16 5 C 20716 2.51 5 N 4764 2.21 5 O 5840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 31541 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7251 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 910, 7243 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 881} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 910, 7243 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 881} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7403 Chain: "B" Number of atoms: 7251 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 910, 7243 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 881} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 910, 7243 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 881} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7403 Chain: "C" Number of atoms: 7251 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 910, 7243 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 881} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 910, 7243 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 881} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7403 Chain: "D" Number of atoms: 7251 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 910, 7243 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 881} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 910, 7243 Classifications: {'peptide': 910} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 881} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 7403 Chain: "A" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 674 Unusual residues: {' K': 6, 'AJP': 9, 'CLR': 1, 'POV': 7} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 520 Unresolved non-hydrogen angles: 725 Unresolved non-hydrogen dihedrals: 912 Unresolved non-hydrogen chiralities: 148 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 632 Unusual residues: {' K': 1, 'AJP': 9, 'CLR': 1, 'POV': 6} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 707 Unresolved non-hydrogen dihedrals: 899 Unresolved non-hydrogen chiralities: 148 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 632 Unusual residues: {' K': 1, 'AJP': 9, 'CLR': 1, 'POV': 6} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 505 Unresolved non-hydrogen angles: 707 Unresolved non-hydrogen dihedrals: 899 Unresolved non-hydrogen chiralities: 148 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 595 Unusual residues: {' K': 1, 'AJP': 9, 'CLR': 1, 'POV': 5} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 490 Unresolved non-hydrogen angles: 689 Unresolved non-hydrogen dihedrals: 886 Unresolved non-hydrogen chiralities: 148 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 1, 'POV:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 30.81, per 1000 atoms: 0.98 Number of scatterers: 31541 At special positions: 0 Unit cell: (169.56, 169.56, 136.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 9 19.00 S 192 16.00 P 20 15.00 O 5840 8.00 N 4764 7.00 C 20716 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: 8.84 Conformation dependent library (CDL) restraints added in 7.2 seconds 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 24 sheets defined 54.8% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.41 Creating SS restraints... Processing helix chain 'A' and resid 21 through 50 removed outlier: 3.599A pdb=" N PHE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 removed outlier: 3.788A pdb=" N ILE A 105 " --> pdb=" O ALA A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 134 Processing helix chain 'A' and resid 148 through 170 removed outlier: 3.535A pdb=" N PHE A 159 " --> pdb=" O ALA A 155 " (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 removed outlier: 3.696A pdb=" N ARG A 210 " --> pdb=" O ARG A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 removed outlier: 3.573A pdb=" N ILE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) 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 removed outlier: 3.572A pdb=" N HIS A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 432 through 451 removed outlier: 3.552A pdb=" N GLU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.566A pdb=" N ILE A 472 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 480 removed outlier: 3.506A pdb=" N GLY A 480 " --> pdb=" O TRP A 477 " (cutoff:3.500A) 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: 4.175A pdb=" N TYR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 531 " --> pdb=" O TYR A 527 " (cutoff:3.500A) removed outlier: 3.685A 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 601 through 609 removed outlier: 3.571A pdb=" N GLU A 604 " --> pdb=" O ASP A 601 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 606 " --> pdb=" O LYS A 603 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ARG A 607 " --> pdb=" O GLU A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 621 through 625 Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 734 through 742 Proline residue: A 740 - end of helix Processing helix chain 'A' and resid 759 through 765 removed outlier: 3.932A pdb=" N ARG A 765 " --> pdb=" O GLU A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 770 Processing helix chain 'A' and resid 785 through 792 Processing helix chain 'A' and resid 817 through 829 Processing helix chain 'A' and resid 872 through 876 removed outlier: 4.006A pdb=" N ASN A 875 " --> pdb=" O THR A 872 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 892 removed outlier: 4.164A pdb=" N GLN A 889 " --> pdb=" O THR A 886 " (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: 3.921A pdb=" N ASP A 921 " --> pdb=" O VAL A 917 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N SER A 925 " --> pdb=" O ASP A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 942 removed outlier: 3.910A 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 972 Processing helix chain 'A' and resid 995 through 1007 removed outlier: 3.663A 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 50 removed outlier: 3.598A pdb=" N PHE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 removed outlier: 3.784A pdb=" N ILE B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 134 Processing helix chain 'B' and resid 148 through 170 removed outlier: 3.536A pdb=" N PHE B 159 " --> pdb=" O ALA B 155 " (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 removed outlier: 3.695A pdb=" N ARG B 210 " --> pdb=" O ARG B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.575A pdb=" N ILE B 220 " --> pdb=" O GLN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 260 Processing helix chain 'B' and resid 261 through 265 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 removed outlier: 3.575A pdb=" N HIS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 Processing helix chain 'B' and resid 432 through 451 removed outlier: 3.550A pdb=" N GLU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.567A pdb=" N ILE B 472 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 removed outlier: 3.506A pdb=" N GLY B 480 " --> pdb=" O TRP B 477 " (cutoff:3.500A) 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: 4.183A pdb=" N TYR B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 531 " --> pdb=" O TYR B 527 " (cutoff:3.500A) removed outlier: 3.747A 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 601 through 609 removed outlier: 3.569A pdb=" N GLU B 604 " --> pdb=" O ASP B 601 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LYS B 606 " --> pdb=" O LYS B 603 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG B 607 " --> pdb=" O GLU B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 617 Processing helix chain 'B' and resid 621 through 625 Processing helix chain 'B' and resid 699 through 703 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 734 through 742 Proline residue: B 740 - end of helix Processing helix chain 'B' and resid 759 through 765 removed outlier: 3.932A pdb=" N ARG B 765 " --> pdb=" O GLU B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 766 through 770 Processing helix chain 'B' and resid 785 through 792 Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'B' and resid 872 through 876 removed outlier: 4.006A pdb=" N ASN B 875 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 892 removed outlier: 4.164A pdb=" N GLN B 889 " --> pdb=" O THR B 886 " (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: 3.923A pdb=" N ASP B 921 " --> pdb=" O VAL B 917 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 925 " --> pdb=" O ASP B 921 " (cutoff:3.500A) Processing helix chain 'B' and resid 931 through 942 removed outlier: 3.909A 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 972 Processing helix chain 'B' and resid 995 through 1007 removed outlier: 3.664A pdb=" N LEU B 999 " --> pdb=" O CYS B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1019 through 1021 No H-bonds generated for 'chain 'B' and resid 1019 through 1021' Processing helix chain 'C' and resid 21 through 50 removed outlier: 3.598A pdb=" N PHE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 29 " --> pdb=" O PHE C 25 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.786A pdb=" N ILE C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 134 Processing helix chain 'C' and resid 148 through 170 removed outlier: 3.537A pdb=" N PHE C 159 " --> pdb=" O ALA C 155 " (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 removed outlier: 3.694A pdb=" N ARG C 210 " --> pdb=" O ARG C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.575A pdb=" N ILE C 220 " --> pdb=" O GLN C 216 " (cutoff:3.500A) 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 removed outlier: 3.575A pdb=" N HIS C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 414 Processing helix chain 'C' and resid 432 through 451 removed outlier: 3.551A pdb=" N GLU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.567A pdb=" N ILE C 472 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 480 removed outlier: 3.506A pdb=" N GLY C 480 " --> pdb=" O TRP C 477 " (cutoff:3.500A) 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: 4.187A pdb=" N TYR C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY C 531 " --> pdb=" O TYR C 527 " (cutoff:3.500A) removed outlier: 3.733A 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 601 through 609 removed outlier: 3.569A pdb=" N GLU C 604 " --> pdb=" O ASP C 601 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C 606 " --> pdb=" O LYS C 603 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG C 607 " --> pdb=" O GLU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 617 Processing helix chain 'C' and resid 621 through 625 Processing helix chain 'C' and resid 699 through 703 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 734 through 742 Proline residue: C 740 - end of helix Processing helix chain 'C' and resid 759 through 765 removed outlier: 3.931A pdb=" N ARG C 765 " --> pdb=" O GLU C 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 770 Processing helix chain 'C' and resid 785 through 792 Processing helix chain 'C' and resid 817 through 829 Processing helix chain 'C' and resid 872 through 876 removed outlier: 4.006A pdb=" N ASN C 875 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 892 removed outlier: 4.165A pdb=" N GLN C 889 " --> pdb=" O THR C 886 " (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: 3.916A pdb=" N ASP C 921 " --> pdb=" O VAL C 917 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N SER C 925 " --> pdb=" O ASP C 921 " (cutoff:3.500A) Processing helix chain 'C' and resid 931 through 942 removed outlier: 3.907A 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 972 Processing helix chain 'C' and resid 995 through 1007 removed outlier: 3.666A pdb=" N LEU C 999 " --> pdb=" O CYS C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1021 No H-bonds generated for 'chain 'C' and resid 1019 through 1021' Processing helix chain 'D' and resid 21 through 50 removed outlier: 3.600A pdb=" N PHE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER D 29 " --> pdb=" O PHE D 25 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLY D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 105 removed outlier: 3.784A pdb=" N ILE D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 134 Processing helix chain 'D' and resid 148 through 170 removed outlier: 3.529A pdb=" N PHE D 159 " --> pdb=" O ALA D 155 " (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 removed outlier: 3.694A pdb=" N ARG D 210 " --> pdb=" O ARG D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.576A pdb=" N ILE D 220 " --> pdb=" O GLN D 216 " (cutoff:3.500A) 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 removed outlier: 3.572A pdb=" N HIS D 394 " --> pdb=" O LEU D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 414 Processing helix chain 'D' and resid 432 through 451 removed outlier: 3.550A pdb=" N GLU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.567A pdb=" N ILE D 472 " --> pdb=" O LEU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 480 removed outlier: 3.506A pdb=" N GLY D 480 " --> pdb=" O TRP D 477 " (cutoff:3.500A) 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: 4.190A pdb=" N TYR D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY D 531 " --> pdb=" O TYR D 527 " (cutoff:3.500A) removed outlier: 3.729A 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 601 through 609 removed outlier: 3.569A pdb=" N GLU D 604 " --> pdb=" O ASP D 601 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS D 606 " --> pdb=" O LYS D 603 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG D 607 " --> pdb=" O GLU D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 617 Processing helix chain 'D' and resid 621 through 625 Processing helix chain 'D' and resid 699 through 703 Processing helix chain 'D' and resid 706 through 713 Processing helix chain 'D' and resid 734 through 742 Proline residue: D 740 - end of helix Processing helix chain 'D' and resid 759 through 765 removed outlier: 3.932A pdb=" N ARG D 765 " --> pdb=" O GLU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 766 through 770 Processing helix chain 'D' and resid 785 through 792 Processing helix chain 'D' and resid 817 through 829 Processing helix chain 'D' and resid 872 through 876 removed outlier: 4.006A pdb=" N ASN D 875 " --> pdb=" O THR D 872 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 892 removed outlier: 4.164A pdb=" N GLN D 889 " --> pdb=" O THR D 886 " (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: 3.923A pdb=" N ASP D 921 " --> pdb=" O VAL D 917 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER D 925 " --> pdb=" O ASP D 921 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 942 removed outlier: 3.909A 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 972 Processing helix chain 'D' and resid 995 through 1007 removed outlier: 3.666A pdb=" N LEU D 999 " --> pdb=" O CYS D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1019 through 1021 No H-bonds generated for 'chain 'D' and resid 1019 through 1021' Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140 Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 402 removed outlier: 4.399A pdb=" N GLY A 349 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N HIS A 344 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N LEU A 423 " --> pdb=" O HIS A 344 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 346 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU A 425 " --> pdb=" O VAL A 346 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N CYS A 348 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N CYS A 422 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLN A 459 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE A 424 " --> pdb=" O GLN A 459 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 456 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE A 484 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.657A 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: 4.330A pdb=" N LEU A 594 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A 567 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE A 598 " --> pdb=" O MET A 565 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N MET A 565 " --> pdb=" O ILE A 598 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 686 through 687 removed outlier: 4.390A 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: 6.379A pdb=" N ILE A 754 " --> pdb=" O SER A 777 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU A 779 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE A 756 " --> pdb=" O LEU A 779 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL A 720 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N LEU A 803 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS A 722 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS A 800 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU A 881 " --> pdb=" O CYS A 800 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE A 802 " --> pdb=" O GLU A 881 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE A 915 " --> pdb=" O ILE A 878 " (cutoff:3.500A) removed outlier: 6.343A 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: 4.211A pdb=" N GLY A1013 " --> pdb=" O PHE A1050 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU A1052 " --> pdb=" O CYS A1011 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N CYS A1011 " --> pdb=" O LEU A1052 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 139 through 140 Processing sheet with id=AA8, first strand: chain 'B' and resid 398 through 402 removed outlier: 4.395A pdb=" N GLY B 349 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N HIS B 344 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N LEU B 423 " --> pdb=" O HIS B 344 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL B 346 " --> pdb=" O LEU B 423 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N LEU B 425 " --> pdb=" O VAL B 346 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N CYS B 348 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS B 422 " --> pdb=" O ILE B 457 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLN B 459 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE B 424 " --> pdb=" O GLN B 459 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE B 456 " --> pdb=" O ASP B 482 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE B 484 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 6.648A 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: 4.346A pdb=" N LEU B 594 " --> pdb=" O GLU B 569 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA B 567 " --> pdb=" O PHE B 596 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE B 598 " --> pdb=" O MET B 565 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N MET B 565 " --> pdb=" O ILE B 598 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 686 through 687 removed outlier: 4.390A 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: 6.379A pdb=" N ILE B 754 " --> pdb=" O SER B 777 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU B 779 " --> pdb=" O ILE B 754 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N PHE B 756 " --> pdb=" O LEU B 779 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 720 " --> pdb=" O VAL B 801 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N LEU B 803 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N CYS B 722 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS B 800 " --> pdb=" O ILE B 879 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU B 881 " --> pdb=" O CYS B 800 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE B 802 " --> pdb=" O GLU B 881 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N PHE B 915 " --> pdb=" O ILE B 878 " (cutoff:3.500A) removed outlier: 6.342A 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: 4.212A pdb=" N GLY B1013 " --> pdb=" O PHE B1050 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU B1052 " --> pdb=" O CYS B1011 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS B1011 " --> pdb=" O LEU B1052 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 139 through 140 Processing sheet with id=AB5, first strand: chain 'C' and resid 398 through 402 removed outlier: 4.394A pdb=" N GLY C 349 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N HIS C 344 " --> pdb=" O ALA C 421 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N LEU C 423 " --> pdb=" O HIS C 344 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL C 346 " --> pdb=" O LEU C 423 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU C 425 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N CYS C 348 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS C 422 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N GLN C 459 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ILE C 424 " --> pdb=" O GLN C 459 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE C 456 " --> pdb=" O ASP C 482 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N ILE C 484 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.648A 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: 4.332A pdb=" N LEU C 594 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C 567 " --> pdb=" O PHE C 596 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE C 598 " --> pdb=" O MET C 565 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N MET C 565 " --> pdb=" O ILE C 598 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 686 through 687 removed outlier: 4.389A 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: 6.380A pdb=" N ILE C 754 " --> pdb=" O SER C 777 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU C 779 " --> pdb=" O ILE C 754 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE C 756 " --> pdb=" O LEU C 779 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL C 720 " --> pdb=" O VAL C 801 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N LEU C 803 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS C 722 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS C 800 " --> pdb=" O ILE C 879 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU C 881 " --> pdb=" O CYS C 800 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE C 802 " --> pdb=" O GLU C 881 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE C 915 " --> pdb=" O ILE C 878 " (cutoff:3.500A) removed outlier: 6.327A 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: 4.212A pdb=" N GLY C1013 " --> pdb=" O PHE C1050 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N LEU C1052 " --> pdb=" O CYS C1011 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N CYS C1011 " --> pdb=" O LEU C1052 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 139 through 140 Processing sheet with id=AC2, first strand: chain 'D' and resid 398 through 402 removed outlier: 4.397A pdb=" N GLY D 349 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N HIS D 344 " --> pdb=" O ALA D 421 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N LEU D 423 " --> pdb=" O HIS D 344 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL D 346 " --> pdb=" O LEU D 423 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU D 425 " --> pdb=" O VAL D 346 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N CYS D 348 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N CYS D 422 " --> pdb=" O ILE D 457 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N GLN D 459 " --> pdb=" O CYS D 422 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N ILE D 424 " --> pdb=" O GLN D 459 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE D 456 " --> pdb=" O ASP D 482 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE D 484 " --> pdb=" O ILE D 456 " (cutoff:3.500A) removed outlier: 6.657A 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: 4.328A pdb=" N LEU D 594 " --> pdb=" O GLU D 569 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA D 567 " --> pdb=" O PHE D 596 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE D 598 " --> pdb=" O MET D 565 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N MET D 565 " --> pdb=" O ILE D 598 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 686 through 687 removed outlier: 4.390A 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: 6.379A pdb=" N ILE D 754 " --> pdb=" O SER D 777 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU D 779 " --> pdb=" O ILE D 754 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE D 756 " --> pdb=" O LEU D 779 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL D 720 " --> pdb=" O VAL D 801 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N LEU D 803 " --> pdb=" O VAL D 720 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N CYS D 722 " --> pdb=" O LEU D 803 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N CYS D 800 " --> pdb=" O ILE D 879 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N GLU D 881 " --> pdb=" O CYS D 800 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ILE D 802 " --> pdb=" O GLU D 881 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N PHE D 915 " --> pdb=" O ILE D 878 " (cutoff:3.500A) removed outlier: 6.342A 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: 4.212A pdb=" N GLY D1013 " --> pdb=" O PHE D1050 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU D1052 " --> pdb=" O CYS D1011 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS D1011 " --> pdb=" O LEU D1052 " (cutoff:3.500A) 1394 hydrogen bonds defined for protein. 3783 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: 12.42 Time building geometry restraints manager: 10.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5056 1.33 - 1.45: 8637 1.45 - 1.57: 18415 1.57 - 1.69: 40 1.69 - 1.81: 284 Bond restraints: 32432 Sorted by residual: bond pdb=" C21 POV B1105 " pdb=" O22 POV B1105 " ideal model delta sigma weight residual 1.205 1.330 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C21 POV B1105 " pdb=" O21 POV B1105 " ideal model delta sigma weight residual 1.330 1.205 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C21 POV A1111 " pdb=" O21 POV A1111 " ideal model delta sigma weight residual 1.330 1.205 0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C21 POV A1111 " pdb=" O22 POV A1111 " ideal model delta sigma weight residual 1.205 1.330 -0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C21 POV D1104 " pdb=" O22 POV D1104 " ideal model delta sigma weight residual 1.205 1.330 -0.125 2.00e-02 2.50e+03 3.90e+01 ... (remaining 32427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.89: 43998 2.89 - 5.78: 414 5.78 - 8.68: 12 8.68 - 11.57: 0 11.57 - 14.46: 8 Bond angle restraints: 44432 Sorted by residual: angle pdb=" C22 POV B1105 " pdb=" C21 POV B1105 " pdb=" O22 POV B1105 " ideal model delta sigma weight residual 125.44 110.98 14.46 3.00e+00 1.11e-01 2.32e+01 angle pdb=" C22 POV D1104 " pdb=" C21 POV D1104 " pdb=" O22 POV D1104 " ideal model delta sigma weight residual 125.44 111.02 14.42 3.00e+00 1.11e-01 2.31e+01 angle pdb=" C22 POV B1105 " pdb=" C21 POV B1105 " pdb=" O21 POV B1105 " ideal model delta sigma weight residual 111.03 125.42 -14.39 3.00e+00 1.11e-01 2.30e+01 angle pdb=" C22 POV C1105 " pdb=" C21 POV C1105 " pdb=" O22 POV C1105 " ideal model delta sigma weight residual 125.44 111.05 14.39 3.00e+00 1.11e-01 2.30e+01 angle pdb=" C22 POV C1105 " pdb=" C21 POV C1105 " pdb=" O21 POV C1105 " ideal model delta sigma weight residual 111.03 125.41 -14.38 3.00e+00 1.11e-01 2.30e+01 ... (remaining 44427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.39: 21337 25.39 - 50.79: 892 50.79 - 76.18: 407 76.18 - 101.58: 204 101.58 - 126.97: 300 Dihedral angle restraints: 23140 sinusoidal: 12464 harmonic: 10676 Sorted by residual: dihedral pdb=" O31 AJP D1108 " pdb=" C30 AJP D1108 " pdb=" C32 AJP D1108 " pdb=" O33 AJP D1108 " ideal model delta sinusoidal sigma weight residual 177.28 -55.75 -126.97 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" O31 AJP C1109 " pdb=" C30 AJP C1109 " pdb=" C32 AJP C1109 " pdb=" O33 AJP C1109 " ideal model delta sinusoidal sigma weight residual 177.28 -55.76 -126.96 1 3.00e+01 1.11e-03 1.71e+01 dihedral pdb=" O31 AJP A1115 " pdb=" C30 AJP A1115 " pdb=" C32 AJP A1115 " pdb=" O33 AJP A1115 " ideal model delta sinusoidal sigma weight residual 177.28 -55.80 -126.92 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 23137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3960 0.043 - 0.086: 1048 0.086 - 0.129: 299 0.129 - 0.173: 46 0.173 - 0.216: 91 Chirality restraints: 5444 Sorted by residual: chirality pdb=" C10 AJP D1115 " pdb=" C08 AJP D1115 " pdb=" C11 AJP D1115 " pdb=" O82 AJP D1115 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C10 AJP B1116 " pdb=" C08 AJP B1116 " pdb=" C11 AJP B1116 " pdb=" O82 AJP B1116 " both_signs ideal model delta sigma weight residual False 2.61 2.39 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" C10 AJP C1116 " pdb=" C08 AJP C1116 " pdb=" C11 AJP C1116 " pdb=" O82 AJP C1116 " both_signs ideal model delta sigma weight residual False 2.61 2.40 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 5441 not shown) Planarity restraints: 5100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 190 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO A 191 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 190 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO D 191 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO D 191 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 191 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 190 " -0.030 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO C 191 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 191 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 191 " -0.025 5.00e-02 4.00e+02 ... (remaining 5097 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.80: 7576 2.80 - 3.38: 33439 3.38 - 3.97: 58269 3.97 - 4.55: 80636 4.55 - 5.14: 120983 Nonbonded interactions: 300903 Sorted by model distance: nonbonded pdb=" OG SER C 804 " pdb=" OE2 GLU C 819 " model vdw 2.210 3.040 nonbonded pdb=" OG SER B 804 " pdb=" OE2 GLU B 819 " model vdw 2.210 3.040 nonbonded pdb=" OG SER D 804 " pdb=" OE2 GLU D 819 " model vdw 2.211 3.040 nonbonded pdb=" OG SER A 804 " pdb=" OE2 GLU A 819 " model vdw 2.211 3.040 nonbonded pdb=" OE1 GLU B 535 " pdb=" OH TYR B 537 " model vdw 2.265 3.040 ... (remaining 300898 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 328 or resid 330 through 1057 or (resid 1114 th \ rough 1115 and (name C01 or name C02 or name C03 or name C04 or name C05 or name \ C06 or name C07 or name C08 or name C10 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24 or name C26 or name C27 or name \ C28 or name C29 or name C30 or name C32 or name C80 or name C81 or name C83 or \ name C85 or name O09 or name O25 or name O31 or name O33 or name O34 or name O77 \ or name O78 or name O79 or name O82 or name O84)))) selection = (chain 'B' and (resid 19 through 328 or resid 330 through 1057 or resid 1114 thr \ ough 1115)) selection = (chain 'C' and (resid 19 through 328 or resid 330 through 1057 or resid 1114 thr \ ough 1115)) selection = (chain 'D' and (resid 19 through 328 or resid 330 through 1057 or (resid 1114 th \ rough 1115 and (name C01 or name C02 or name C03 or name C04 or name C05 or name \ C06 or name C07 or name C08 or name C10 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24 or name C26 or name C27 or name \ C28 or name C29 or name C30 or name C32 or name C80 or name C81 or name C83 or \ name C85 or name O09 or name O25 or name O31 or name O33 or name O34 or name O77 \ or name O78 or name O79 or name O82 or name O84)))) } 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.050 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 88.830 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 32432 Z= 0.212 Angle : 0.647 14.459 44432 Z= 0.282 Chirality : 0.048 0.216 5444 Planarity : 0.004 0.045 5100 Dihedral : 23.548 126.973 16228 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 0.66 (0.14), residues: 3612 helix: 0.67 (0.12), residues: 1732 sheet: 0.16 (0.25), residues: 472 loop : 0.50 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 100 HIS 0.003 0.001 HIS C 616 PHE 0.024 0.001 PHE B 391 TYR 0.020 0.001 TYR A1015 ARG 0.004 0.000 ARG B 607 Details of bonding type rmsd hydrogen bonds : bond 0.16188 ( 1394) hydrogen bonds : angle 5.48814 ( 3783) covalent geometry : bond 0.00429 (32432) covalent geometry : angle 0.64685 (44432) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 3.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.9057 (mtm) cc_final: 0.8820 (mtm) REVERT: A 285 MET cc_start: 0.8715 (mmp) cc_final: 0.8033 (mtm) REVERT: A 314 MET cc_start: 0.8200 (mtp) cc_final: 0.7857 (mtp) REVERT: A 893 GLN cc_start: 0.8831 (mt0) cc_final: 0.8624 (mm-40) REVERT: B 154 MET cc_start: 0.9046 (mtm) cc_final: 0.8828 (mtm) REVERT: B 285 MET cc_start: 0.8731 (mmp) cc_final: 0.7959 (mtm) REVERT: B 314 MET cc_start: 0.8182 (mtp) cc_final: 0.7851 (mtp) REVERT: C 154 MET cc_start: 0.9036 (mtm) cc_final: 0.8800 (mtm) REVERT: C 285 MET cc_start: 0.8733 (mmp) cc_final: 0.7964 (mtm) REVERT: C 314 MET cc_start: 0.8188 (mtp) cc_final: 0.7852 (mtp) REVERT: D 154 MET cc_start: 0.9040 (mtm) cc_final: 0.8708 (mtm) REVERT: D 285 MET cc_start: 0.8569 (mmp) cc_final: 0.7955 (mtm) REVERT: D 314 MET cc_start: 0.8208 (mtp) cc_final: 0.7866 (mtp) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 1.5698 time to fit residues: 352.8817 Evaluate side-chains 128 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 307 optimal weight: 5.9990 chunk 275 optimal weight: 10.0000 chunk 153 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 285 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 chunk 173 optimal weight: 6.9990 chunk 212 optimal weight: 0.8980 chunk 330 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN B 157 ASN B 328 ASN B 590 GLN C 157 ASN C 328 ASN D 157 ASN D 328 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.084328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.055628 restraints weight = 94139.492| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.27 r_work: 0.2785 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32432 Z= 0.176 Angle : 0.701 8.841 44432 Z= 0.309 Chirality : 0.045 0.285 5444 Planarity : 0.004 0.042 5100 Dihedral : 15.345 124.559 9532 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.50 % Allowed : 3.33 % Favored : 96.17 % 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: 0.90 (0.14), residues: 3612 helix: 0.82 (0.12), residues: 1800 sheet: 0.42 (0.26), residues: 464 loop : 0.61 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 275 HIS 0.004 0.001 HIS A 350 PHE 0.030 0.002 PHE D 303 TYR 0.024 0.002 TYR B1015 ARG 0.009 0.001 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 1394) hydrogen bonds : angle 4.47079 ( 3783) covalent geometry : bond 0.00417 (32432) covalent geometry : angle 0.70065 (44432) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 MET cc_start: 0.8942 (mtm) cc_final: 0.8633 (mtm) REVERT: A 285 MET cc_start: 0.8616 (mmp) cc_final: 0.7966 (mtm) REVERT: B 285 MET cc_start: 0.8602 (mmp) cc_final: 0.7856 (mtm) REVERT: C 154 MET cc_start: 0.8941 (mtm) cc_final: 0.8628 (mtm) REVERT: C 285 MET cc_start: 0.8670 (mmp) cc_final: 0.7866 (mtm) REVERT: D 154 MET cc_start: 0.8939 (mtm) cc_final: 0.8625 (mtm) REVERT: D 285 MET cc_start: 0.8679 (mmp) cc_final: 0.7873 (mtm) outliers start: 16 outliers final: 5 residues processed: 146 average time/residue: 1.4978 time to fit residues: 259.5698 Evaluate side-chains 125 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 120 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 331 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 302 optimal weight: 5.9990 chunk 314 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 178 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 305 optimal weight: 0.7980 chunk 216 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 GLN A 328 ASN B 328 ASN C 328 ASN C 409 HIS D 142 GLN D 328 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.084388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.055716 restraints weight = 131922.290| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.68 r_work: 0.2766 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32432 Z= 0.129 Angle : 0.585 9.507 44432 Z= 0.264 Chirality : 0.041 0.296 5444 Planarity : 0.004 0.038 5100 Dihedral : 10.923 115.626 9532 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.53 % Allowed : 4.24 % Favored : 95.23 % 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: 1.12 (0.14), residues: 3612 helix: 1.05 (0.12), residues: 1800 sheet: 0.45 (0.26), residues: 472 loop : 0.65 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 275 HIS 0.002 0.001 HIS A 350 PHE 0.026 0.001 PHE A 303 TYR 0.016 0.001 TYR B1015 ARG 0.005 0.000 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.04113 ( 1394) hydrogen bonds : angle 4.25558 ( 3783) covalent geometry : bond 0.00303 (32432) covalent geometry : angle 0.58486 (44432) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 3.401 Fit side-chains REVERT: A 154 MET cc_start: 0.8879 (mtm) cc_final: 0.8610 (mtm) REVERT: A 285 MET cc_start: 0.8602 (mmp) cc_final: 0.7949 (mtm) REVERT: B 154 MET cc_start: 0.8972 (mtm) cc_final: 0.8583 (mtm) REVERT: B 285 MET cc_start: 0.8670 (mmp) cc_final: 0.7849 (mtm) REVERT: C 154 MET cc_start: 0.8882 (mtm) cc_final: 0.8608 (mtm) REVERT: C 285 MET cc_start: 0.8700 (mmp) cc_final: 0.7866 (mtm) REVERT: D 154 MET cc_start: 0.8872 (mtm) cc_final: 0.8604 (mtm) REVERT: D 285 MET cc_start: 0.8691 (mmp) cc_final: 0.7872 (mtm) outliers start: 17 outliers final: 8 residues processed: 138 average time/residue: 1.4203 time to fit residues: 235.2872 Evaluate side-chains 131 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 628 CYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 628 CYS Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 628 CYS Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 173 optimal weight: 10.0000 chunk 131 optimal weight: 0.8980 chunk 264 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 356 optimal weight: 2.9990 chunk 340 optimal weight: 8.9990 chunk 307 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 957 ASN B 328 ASN B 957 ASN C 142 GLN C 328 ASN C 957 ASN D 328 ASN D 957 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.084538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.056235 restraints weight = 111680.137| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.44 r_work: 0.2783 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 32432 Z= 0.115 Angle : 0.533 9.814 44432 Z= 0.247 Chirality : 0.039 0.219 5444 Planarity : 0.003 0.040 5100 Dihedral : 9.515 114.838 9532 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.60 % Allowed : 5.03 % Favored : 94.38 % 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: 1.26 (0.14), residues: 3612 helix: 1.18 (0.12), residues: 1800 sheet: 0.51 (0.26), residues: 472 loop : 0.70 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 275 HIS 0.002 0.001 HIS D 350 PHE 0.023 0.001 PHE D 303 TYR 0.014 0.001 TYR A1015 ARG 0.005 0.000 ARG C 393 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 1394) hydrogen bonds : angle 4.13507 ( 3783) covalent geometry : bond 0.00268 (32432) covalent geometry : angle 0.53330 (44432) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 3.528 Fit side-chains REVERT: A 285 MET cc_start: 0.8538 (mmp) cc_final: 0.7890 (mtm) REVERT: B 154 MET cc_start: 0.8873 (mtm) cc_final: 0.8491 (mtm) REVERT: B 285 MET cc_start: 0.8646 (mmp) cc_final: 0.7825 (mtm) REVERT: C 285 MET cc_start: 0.8674 (mmp) cc_final: 0.7845 (mtm) REVERT: D 285 MET cc_start: 0.8632 (mmp) cc_final: 0.7794 (mtm) outliers start: 19 outliers final: 10 residues processed: 143 average time/residue: 1.4281 time to fit residues: 245.3062 Evaluate side-chains 137 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 628 CYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 628 CYS Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 628 CYS Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 245 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 152 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 325 optimal weight: 3.9990 chunk 362 optimal weight: 7.9990 chunk 353 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 957 ASN B 142 GLN B 328 ASN B 957 ASN C 328 ASN C 957 ASN D 328 ASN D 957 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.083116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.054349 restraints weight = 122115.968| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.60 r_work: 0.2741 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32432 Z= 0.162 Angle : 0.549 11.012 44432 Z= 0.260 Chirality : 0.040 0.155 5444 Planarity : 0.004 0.037 5100 Dihedral : 8.861 105.439 9532 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.63 % Allowed : 5.62 % Favored : 93.75 % 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: 1.20 (0.14), residues: 3612 helix: 1.16 (0.12), residues: 1800 sheet: 0.50 (0.26), residues: 472 loop : 0.64 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 275 HIS 0.004 0.001 HIS A 350 PHE 0.015 0.001 PHE C 511 TYR 0.016 0.001 TYR B1015 ARG 0.003 0.000 ARG D 765 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 1394) hydrogen bonds : angle 4.25733 ( 3783) covalent geometry : bond 0.00390 (32432) covalent geometry : angle 0.54939 (44432) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 3.317 Fit side-chains REVERT: A 285 MET cc_start: 0.8766 (mmp) cc_final: 0.8075 (mtm) REVERT: A 372 ASN cc_start: 0.7755 (m-40) cc_final: 0.7483 (m110) REVERT: A 1009 MET cc_start: 0.8960 (ttp) cc_final: 0.8682 (ttp) REVERT: B 154 MET cc_start: 0.8901 (mtm) cc_final: 0.8466 (mtm) REVERT: B 285 MET cc_start: 0.8763 (mmp) cc_final: 0.7989 (mtm) REVERT: B 372 ASN cc_start: 0.7757 (m-40) cc_final: 0.7484 (m110) REVERT: B 1009 MET cc_start: 0.8960 (ttp) cc_final: 0.8681 (ttp) REVERT: C 285 MET cc_start: 0.8756 (mmp) cc_final: 0.7974 (mtm) REVERT: C 372 ASN cc_start: 0.7753 (m-40) cc_final: 0.7477 (m110) REVERT: C 1009 MET cc_start: 0.8954 (ttp) cc_final: 0.8676 (ttp) REVERT: D 285 MET cc_start: 0.8693 (mmp) cc_final: 0.7860 (mtm) REVERT: D 372 ASN cc_start: 0.7747 (m-40) cc_final: 0.7472 (m110) REVERT: D 1009 MET cc_start: 0.8958 (ttp) cc_final: 0.8681 (ttp) outliers start: 20 outliers final: 11 residues processed: 144 average time/residue: 1.4302 time to fit residues: 246.3761 Evaluate side-chains 138 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 628 CYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 628 CYS Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 628 CYS Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 316 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 354 optimal weight: 0.3980 chunk 253 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 357 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 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 328 ASN A 957 ASN B 328 ASN B 957 ASN C 328 ASN C 957 ASN D 328 ASN D 957 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.084232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.055389 restraints weight = 139685.025| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 3.81 r_work: 0.2761 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2752 r_free = 0.2752 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32432 Z= 0.106 Angle : 0.503 11.276 44432 Z= 0.239 Chirality : 0.038 0.140 5444 Planarity : 0.003 0.039 5100 Dihedral : 8.626 111.322 9532 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.72 % Allowed : 5.68 % Favored : 93.59 % 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: 1.38 (0.14), residues: 3612 helix: 1.31 (0.12), residues: 1804 sheet: 0.62 (0.26), residues: 472 loop : 0.70 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 275 HIS 0.002 0.000 HIS D 254 PHE 0.016 0.001 PHE D 511 TYR 0.011 0.001 TYR A1015 ARG 0.004 0.000 ARG D 393 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 1394) hydrogen bonds : angle 4.07859 ( 3783) covalent geometry : bond 0.00248 (32432) covalent geometry : angle 0.50306 (44432) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 3.321 Fit side-chains REVERT: A 285 MET cc_start: 0.8643 (mmp) cc_final: 0.8047 (mtm) REVERT: A 372 ASN cc_start: 0.7705 (m-40) cc_final: 0.7370 (m110) REVERT: A 1009 MET cc_start: 0.8863 (ttp) cc_final: 0.8533 (ttp) REVERT: B 154 MET cc_start: 0.8884 (mtm) cc_final: 0.8407 (mtm) REVERT: B 285 MET cc_start: 0.8733 (mmp) cc_final: 0.7900 (mtm) REVERT: B 372 ASN cc_start: 0.7698 (m-40) cc_final: 0.7362 (m110) REVERT: B 1009 MET cc_start: 0.8858 (ttp) cc_final: 0.8524 (ttp) REVERT: C 285 MET cc_start: 0.8728 (mmp) cc_final: 0.7895 (mtm) REVERT: C 372 ASN cc_start: 0.7721 (m-40) cc_final: 0.7388 (m110) REVERT: C 1009 MET cc_start: 0.8862 (ttp) cc_final: 0.8533 (ttp) REVERT: D 285 MET cc_start: 0.8662 (mmp) cc_final: 0.7851 (mtm) REVERT: D 372 ASN cc_start: 0.7716 (m-40) cc_final: 0.7383 (m110) REVERT: D 1009 MET cc_start: 0.8856 (ttp) cc_final: 0.8528 (ttp) outliers start: 23 outliers final: 10 residues processed: 143 average time/residue: 1.3446 time to fit residues: 231.3714 Evaluate side-chains 137 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 628 CYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 628 CYS Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 628 CYS Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 343 optimal weight: 8.9990 chunk 89 optimal weight: 0.2980 chunk 75 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 chunk 95 optimal weight: 5.9990 chunk 362 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 303 optimal weight: 10.0000 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN B 328 ASN C 328 ASN D 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.083508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.054713 restraints weight = 139900.936| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.78 r_work: 0.2730 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 32432 Z= 0.141 Angle : 0.527 12.632 44432 Z= 0.251 Chirality : 0.039 0.149 5444 Planarity : 0.003 0.037 5100 Dihedral : 8.549 110.081 9532 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.44 % Allowed : 6.31 % Favored : 93.25 % 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: 1.34 (0.14), residues: 3612 helix: 1.27 (0.12), residues: 1804 sheet: 0.66 (0.26), residues: 464 loop : 0.67 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 275 HIS 0.003 0.001 HIS A 350 PHE 0.015 0.001 PHE C 511 TYR 0.014 0.001 TYR B1015 ARG 0.005 0.000 ARG C 575 Details of bonding type rmsd hydrogen bonds : bond 0.04048 ( 1394) hydrogen bonds : angle 4.15916 ( 3783) covalent geometry : bond 0.00341 (32432) covalent geometry : angle 0.52725 (44432) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 3.775 Fit side-chains REVERT: A 285 MET cc_start: 0.8725 (mmp) cc_final: 0.8021 (mtm) REVERT: A 372 ASN cc_start: 0.7694 (m-40) cc_final: 0.7361 (m110) REVERT: A 1009 MET cc_start: 0.8950 (ttp) cc_final: 0.8640 (ttp) REVERT: B 154 MET cc_start: 0.8880 (mtm) cc_final: 0.8397 (mtm) REVERT: B 285 MET cc_start: 0.8750 (mmp) cc_final: 0.7967 (mtm) REVERT: B 372 ASN cc_start: 0.7701 (m-40) cc_final: 0.7367 (m110) REVERT: B 1009 MET cc_start: 0.8923 (ttp) cc_final: 0.8624 (ttp) REVERT: C 285 MET cc_start: 0.8773 (mmp) cc_final: 0.7992 (mtm) REVERT: C 372 ASN cc_start: 0.7717 (m-40) cc_final: 0.7398 (m110) REVERT: C 1009 MET cc_start: 0.8917 (ttp) cc_final: 0.8623 (ttp) REVERT: D 285 MET cc_start: 0.8697 (mmp) cc_final: 0.7852 (mtm) REVERT: D 372 ASN cc_start: 0.7706 (m-40) cc_final: 0.7388 (m110) REVERT: D 1009 MET cc_start: 0.8916 (ttp) cc_final: 0.8620 (ttp) outliers start: 14 outliers final: 10 residues processed: 145 average time/residue: 1.3846 time to fit residues: 243.1219 Evaluate side-chains 137 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 628 CYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 628 CYS Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 628 CYS Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 81 optimal weight: 1.9990 chunk 231 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 271 optimal weight: 4.9990 chunk 354 optimal weight: 8.9990 chunk 301 optimal weight: 10.0000 chunk 287 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 215 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.082708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.053904 restraints weight = 131923.989| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.69 r_work: 0.2716 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2710 r_free = 0.2710 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 32432 Z= 0.178 Angle : 0.551 12.469 44432 Z= 0.264 Chirality : 0.040 0.160 5444 Planarity : 0.004 0.037 5100 Dihedral : 8.465 109.049 9532 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.50 % Allowed : 6.19 % Favored : 93.31 % 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: 1.08 (0.14), residues: 3612 helix: 1.04 (0.12), residues: 1844 sheet: 0.70 (0.27), residues: 448 loop : 0.47 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 275 HIS 0.003 0.001 HIS D 350 PHE 0.014 0.001 PHE D 303 TYR 0.014 0.001 TYR A1015 ARG 0.005 0.000 ARG C 575 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 1394) hydrogen bonds : angle 4.27027 ( 3783) covalent geometry : bond 0.00432 (32432) covalent geometry : angle 0.55107 (44432) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 3.214 Fit side-chains REVERT: A 285 MET cc_start: 0.8781 (mmp) cc_final: 0.8003 (mtm) REVERT: A 372 ASN cc_start: 0.7717 (m-40) cc_final: 0.7418 (m110) REVERT: A 1009 MET cc_start: 0.8986 (ttp) cc_final: 0.8731 (ttp) REVERT: B 154 MET cc_start: 0.8879 (mtm) cc_final: 0.8424 (mtm) REVERT: B 285 MET cc_start: 0.8746 (mmp) cc_final: 0.7994 (mtm) REVERT: B 372 ASN cc_start: 0.7725 (m-40) cc_final: 0.7428 (m110) REVERT: B 1009 MET cc_start: 0.8975 (ttp) cc_final: 0.8716 (ttp) REVERT: C 285 MET cc_start: 0.8748 (mmp) cc_final: 0.7987 (mtm) REVERT: C 372 ASN cc_start: 0.7710 (m-40) cc_final: 0.7410 (m110) REVERT: C 1009 MET cc_start: 0.8976 (ttp) cc_final: 0.8721 (ttp) REVERT: D 285 MET cc_start: 0.8704 (mmp) cc_final: 0.7914 (mtm) REVERT: D 372 ASN cc_start: 0.7725 (m-40) cc_final: 0.7431 (m110) REVERT: D 1009 MET cc_start: 0.8977 (ttp) cc_final: 0.8725 (ttp) outliers start: 16 outliers final: 10 residues processed: 137 average time/residue: 1.4270 time to fit residues: 234.5252 Evaluate side-chains 137 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 3.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 628 CYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 628 CYS Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 628 CYS Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 224 optimal weight: 1.9990 chunk 203 optimal weight: 0.8980 chunk 361 optimal weight: 4.9990 chunk 346 optimal weight: 5.9990 chunk 280 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 273 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** 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 = 0.3583 r_free = 0.3583 target = 0.083929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.055827 restraints weight = 104166.073| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.34 r_work: 0.2779 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2773 r_free = 0.2773 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32432 Z= 0.111 Angle : 0.508 13.286 44432 Z= 0.242 Chirality : 0.038 0.138 5444 Planarity : 0.003 0.038 5100 Dihedral : 8.290 109.276 9532 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.35 % Allowed : 6.44 % Favored : 93.22 % 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: 1.40 (0.14), residues: 3612 helix: 1.33 (0.12), residues: 1804 sheet: 0.81 (0.27), residues: 452 loop : 0.62 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 275 HIS 0.002 0.000 HIS D 254 PHE 0.016 0.001 PHE A 511 TYR 0.011 0.001 TYR A1015 ARG 0.005 0.000 ARG A 575 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 1394) hydrogen bonds : angle 4.10411 ( 3783) covalent geometry : bond 0.00260 (32432) covalent geometry : angle 0.50756 (44432) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 3.261 Fit side-chains REVERT: A 285 MET cc_start: 0.8704 (mmp) cc_final: 0.8034 (mtm) REVERT: A 372 ASN cc_start: 0.7663 (m-40) cc_final: 0.7346 (m110) REVERT: A 1009 MET cc_start: 0.8858 (ttp) cc_final: 0.8575 (ttp) REVERT: B 154 MET cc_start: 0.8851 (mtm) cc_final: 0.8389 (mtm) REVERT: B 285 MET cc_start: 0.8685 (mmp) cc_final: 0.7944 (mtm) REVERT: B 372 ASN cc_start: 0.7668 (m-40) cc_final: 0.7351 (m110) REVERT: B 1009 MET cc_start: 0.8850 (ttp) cc_final: 0.8563 (ttp) REVERT: C 285 MET cc_start: 0.8708 (mmp) cc_final: 0.7964 (mtm) REVERT: C 372 ASN cc_start: 0.7677 (m-40) cc_final: 0.7362 (m110) REVERT: C 1009 MET cc_start: 0.8847 (ttp) cc_final: 0.8561 (ttp) REVERT: D 285 MET cc_start: 0.8620 (mmp) cc_final: 0.7829 (mtm) REVERT: D 372 ASN cc_start: 0.7673 (m-40) cc_final: 0.7358 (m110) REVERT: D 1009 MET cc_start: 0.8850 (ttp) cc_final: 0.8565 (ttp) outliers start: 11 outliers final: 10 residues processed: 135 average time/residue: 1.4844 time to fit residues: 239.4120 Evaluate side-chains 137 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 3.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 628 CYS Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 628 CYS Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 628 CYS Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 628 CYS Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 152 optimal weight: 0.7980 chunk 316 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 254 optimal weight: 4.9990 chunk 12 optimal weight: 8.9990 chunk 320 optimal weight: 1.9990 chunk 237 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 323 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** 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 = 0.3591 r_free = 0.3591 target = 0.084273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.056137 restraints weight = 103832.569| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.38 r_work: 0.2789 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 32432 Z= 0.099 Angle : 0.497 12.419 44432 Z= 0.240 Chirality : 0.037 0.133 5444 Planarity : 0.003 0.038 5100 Dihedral : 8.208 108.823 9532 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.19 % Allowed : 6.63 % Favored : 93.18 % 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: 1.39 (0.14), residues: 3612 helix: 1.30 (0.12), residues: 1804 sheet: 0.83 (0.27), residues: 452 loop : 0.64 (0.17), residues: 1356 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 0.016 0.001 PHE C 511 TYR 0.011 0.001 TYR A1015 ARG 0.005 0.000 ARG D 575 Details of bonding type rmsd hydrogen bonds : bond 0.03601 ( 1394) hydrogen bonds : angle 4.06539 ( 3783) covalent geometry : bond 0.00226 (32432) covalent geometry : angle 0.49660 (44432) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 3.170 Fit side-chains REVERT: A 285 MET cc_start: 0.8636 (mmp) cc_final: 0.7974 (mtm) REVERT: A 372 ASN cc_start: 0.7699 (m-40) cc_final: 0.7387 (m110) REVERT: A 1009 MET cc_start: 0.8843 (ttp) cc_final: 0.8554 (ttp) REVERT: B 154 MET cc_start: 0.8852 (mtm) cc_final: 0.8396 (mtm) REVERT: B 285 MET cc_start: 0.8691 (mmp) cc_final: 0.7909 (mtm) REVERT: B 372 ASN cc_start: 0.7700 (m-40) cc_final: 0.7388 (m110) REVERT: B 1009 MET cc_start: 0.8838 (ttp) cc_final: 0.8554 (ttp) REVERT: C 285 MET cc_start: 0.8722 (mmp) cc_final: 0.7943 (mtm) REVERT: C 372 ASN cc_start: 0.7710 (m-40) cc_final: 0.7400 (m110) REVERT: C 1009 MET cc_start: 0.8835 (ttp) cc_final: 0.8544 (ttp) REVERT: D 285 MET cc_start: 0.8577 (mmp) cc_final: 0.7729 (mtm) REVERT: D 372 ASN cc_start: 0.7706 (m-40) cc_final: 0.7395 (m110) REVERT: D 1009 MET cc_start: 0.8835 (ttp) cc_final: 0.8545 (ttp) outliers start: 6 outliers final: 6 residues processed: 131 average time/residue: 1.5971 time to fit residues: 251.5875 Evaluate side-chains 133 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 127 time to evaluate : 3.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain C residue 691 MET Chi-restraints excluded: chain C residue 983 LEU Chi-restraints excluded: chain D residue 691 MET Chi-restraints excluded: chain D residue 983 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 215 optimal weight: 0.9990 chunk 297 optimal weight: 0.3980 chunk 211 optimal weight: 7.9990 chunk 288 optimal weight: 7.9990 chunk 251 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 254 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 231 optimal weight: 0.0870 chunk 98 optimal weight: 0.0670 overall best weight: 1.3100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** 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 = 0.3598 r_free = 0.3598 target = 0.084677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.056751 restraints weight = 97302.076| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.28 r_work: 0.2805 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 32432 Z= 0.097 Angle : 0.488 12.395 44432 Z= 0.235 Chirality : 0.037 0.133 5444 Planarity : 0.003 0.039 5100 Dihedral : 8.057 105.769 9532 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.19 % Allowed : 6.72 % Favored : 93.09 % 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: 1.43 (0.14), residues: 3612 helix: 1.34 (0.12), residues: 1804 sheet: 0.85 (0.27), residues: 452 loop : 0.65 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 275 HIS 0.002 0.000 HIS D 254 PHE 0.016 0.001 PHE C 511 TYR 0.010 0.001 TYR C1015 ARG 0.004 0.000 ARG D 575 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 1394) hydrogen bonds : angle 3.97061 ( 3783) covalent geometry : bond 0.00223 (32432) covalent geometry : angle 0.48772 (44432) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22406.30 seconds wall clock time: 387 minutes 31.26 seconds (23251.26 seconds total)