Starting phenix.real_space_refine on Mon Aug 25 23:48:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v64_42989/08_2025/8v64_42989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v64_42989/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8v64_42989/08_2025/8v64_42989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v64_42989/08_2025/8v64_42989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v64_42989/08_2025/8v64_42989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v64_42989/08_2025/8v64_42989.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} 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-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} 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-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} 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-1': 2, 'POV:plan-2': 1, 'POV:plan-3': 1} 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: 10.99, per 1000 atoms: 0.35 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: 2.33 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.08 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: 6.14 Time building geometry restraints manager: 3.14 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 32.040 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.720 ------------------------------------------------------------------------------- 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 : 3.04 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG B 607 TYR 0.020 0.001 TYR A1015 PHE 0.024 0.001 PHE B 391 TRP 0.018 0.001 TRP B 100 HIS 0.003 0.001 HIS C 616 Details of bonding type rmsd covalent geometry : bond 0.00429 (32432) covalent geometry : angle 0.64685 (44432) hydrogen bonds : bond 0.16188 ( 1394) hydrogen bonds : angle 5.48814 ( 3783) *********************** 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 : 0.844 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: 0.6365 time to fit residues: 142.2226 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 : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS A 328 ASN B 157 ASN B 328 ASN B 590 GLN C 157 ASN C 328 ASN D 157 ASN D 254 HIS D 328 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.085299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.056425 restraints weight = 105742.757| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 3.47 r_work: 0.2804 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2799 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2799 r_free = 0.2799 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 = 0.2799 r_free = 0.2799 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2799 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32432 Z= 0.139 Angle : 0.666 8.928 44432 Z= 0.293 Chirality : 0.044 0.278 5444 Planarity : 0.004 0.043 5100 Dihedral : 14.866 123.651 9532 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.50 % Allowed : 3.23 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.14), residues: 3612 helix: 0.91 (0.12), residues: 1800 sheet: 0.42 (0.26), residues: 464 loop : 0.66 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 393 TYR 0.021 0.001 TYR A1015 PHE 0.028 0.002 PHE D 303 TRP 0.012 0.001 TRP B 100 HIS 0.003 0.001 HIS A 365 Details of bonding type rmsd covalent geometry : bond 0.00322 (32432) covalent geometry : angle 0.66605 (44432) hydrogen bonds : bond 0.03948 ( 1394) hydrogen bonds : angle 4.36784 ( 3783) *********************** 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 160 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.876 Fit side-chains REVERT: A 154 MET cc_start: 0.8948 (mtm) cc_final: 0.8652 (mtm) REVERT: A 285 MET cc_start: 0.8597 (mmp) cc_final: 0.7958 (mtm) REVERT: A 893 GLN cc_start: 0.8877 (mt0) cc_final: 0.8671 (mm-40) REVERT: B 154 MET cc_start: 0.8952 (mtm) cc_final: 0.8649 (mtm) REVERT: B 285 MET cc_start: 0.8586 (mmp) cc_final: 0.7814 (mtm) REVERT: C 154 MET cc_start: 0.8945 (mtm) cc_final: 0.8647 (mtm) REVERT: C 285 MET cc_start: 0.8589 (mmp) cc_final: 0.7842 (mtm) REVERT: D 154 MET cc_start: 0.8949 (mtm) cc_final: 0.8645 (mtm) REVERT: D 285 MET cc_start: 0.8611 (mmp) cc_final: 0.7863 (mtm) outliers start: 16 outliers final: 8 residues processed: 156 average time/residue: 0.5223 time to fit residues: 97.3913 Evaluate side-chains 130 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 297 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 315 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 267 optimal weight: 7.9990 chunk 343 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 210 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 20.0000 chunk 304 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 D 142 GLN D 328 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.083540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.054876 restraints weight = 119210.618| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.55 r_work: 0.2750 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 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 = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 32432 Z= 0.176 Angle : 0.613 9.393 44432 Z= 0.279 Chirality : 0.042 0.302 5444 Planarity : 0.004 0.038 5100 Dihedral : 11.060 116.700 9532 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.63 % Allowed : 3.96 % Favored : 95.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.14), residues: 3612 helix: 0.97 (0.12), residues: 1800 sheet: 0.40 (0.26), residues: 472 loop : 0.65 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 765 TYR 0.019 0.001 TYR A1015 PHE 0.030 0.002 PHE B 303 TRP 0.012 0.001 TRP D 275 HIS 0.004 0.001 HIS C 350 Details of bonding type rmsd covalent geometry : bond 0.00420 (32432) covalent geometry : angle 0.61273 (44432) hydrogen bonds : bond 0.04604 ( 1394) hydrogen bonds : angle 4.38260 ( 3783) *********************** 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: 20 poor density : 123 time to evaluate : 1.104 Fit side-chains REVERT: A 154 MET cc_start: 0.8890 (mtm) cc_final: 0.8613 (mtm) REVERT: A 285 MET cc_start: 0.8673 (mmp) cc_final: 0.7999 (mtm) REVERT: B 154 MET cc_start: 0.8875 (mtm) cc_final: 0.8604 (mtm) REVERT: B 285 MET cc_start: 0.8737 (mmp) cc_final: 0.7930 (mtm) REVERT: C 154 MET cc_start: 0.8874 (mtm) cc_final: 0.8604 (mtm) REVERT: C 285 MET cc_start: 0.8735 (mmp) cc_final: 0.7928 (mtm) REVERT: D 154 MET cc_start: 0.8877 (mtm) cc_final: 0.8606 (mtm) REVERT: D 285 MET cc_start: 0.8747 (mmp) cc_final: 0.7933 (mtm) outliers start: 20 outliers final: 8 residues processed: 135 average time/residue: 0.5772 time to fit residues: 93.2838 Evaluate side-chains 130 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 100 optimal weight: 9.9990 chunk 190 optimal weight: 10.0000 chunk 254 optimal weight: 3.9990 chunk 7 optimal weight: 0.4980 chunk 317 optimal weight: 7.9990 chunk 291 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 320 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.083969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.055374 restraints weight = 125824.493| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.61 r_work: 0.2752 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 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 = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 32432 Z= 0.136 Angle : 0.536 10.072 44432 Z= 0.251 Chirality : 0.039 0.203 5444 Planarity : 0.003 0.039 5100 Dihedral : 9.364 114.050 9532 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.50 % Allowed : 4.81 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.14), residues: 3612 helix: 1.17 (0.12), residues: 1800 sheet: 0.44 (0.26), residues: 472 loop : 0.66 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 393 TYR 0.016 0.001 TYR A1015 PHE 0.025 0.001 PHE C 303 TRP 0.011 0.001 TRP D 275 HIS 0.002 0.001 HIS A 350 Details of bonding type rmsd covalent geometry : bond 0.00325 (32432) covalent geometry : angle 0.53648 (44432) hydrogen bonds : bond 0.03945 ( 1394) hydrogen bonds : angle 4.19661 ( 3783) *********************** 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: 16 poor density : 134 time to evaluate : 1.047 Fit side-chains REVERT: A 285 MET cc_start: 0.8581 (mmp) cc_final: 0.7951 (mtm) REVERT: A 372 ASN cc_start: 0.7755 (m-40) cc_final: 0.7462 (m110) REVERT: B 285 MET cc_start: 0.8664 (mmp) cc_final: 0.7828 (mtm) REVERT: B 372 ASN cc_start: 0.7756 (m-40) cc_final: 0.7463 (m110) REVERT: C 285 MET cc_start: 0.8658 (mmp) cc_final: 0.7821 (mtm) REVERT: C 372 ASN cc_start: 0.7771 (m-40) cc_final: 0.7407 (m110) REVERT: D 285 MET cc_start: 0.8662 (mmp) cc_final: 0.7859 (mtm) REVERT: D 372 ASN cc_start: 0.7767 (m-40) cc_final: 0.7476 (m110) outliers start: 16 outliers final: 8 residues processed: 146 average time/residue: 0.6020 time to fit residues: 104.9194 Evaluate side-chains 138 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 130 time to evaluate : 1.019 ------------------------------------------------------------------------------- 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 258 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 141 optimal weight: 8.9990 chunk 52 optimal weight: 0.0770 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 0.4980 chunk 262 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 231 optimal weight: 8.9990 chunk 281 optimal weight: 8.9990 overall best weight: 4.7144 ------------------------------------------------------------------------------- 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 = 0.3550 r_free = 0.3550 target = 0.082213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.053564 restraints weight = 121571.984| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.56 r_work: 0.2707 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 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 = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32432 Z= 0.222 Angle : 0.588 10.230 44432 Z= 0.281 Chirality : 0.041 0.171 5444 Planarity : 0.004 0.038 5100 Dihedral : 8.983 108.460 9532 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.75 % Allowed : 5.53 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.14), residues: 3612 helix: 0.85 (0.12), residues: 1844 sheet: 0.39 (0.26), residues: 468 loop : 0.50 (0.17), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 765 TYR 0.019 0.001 TYR C1015 PHE 0.017 0.002 PHE A 303 TRP 0.012 0.001 TRP A 275 HIS 0.004 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00538 (32432) covalent geometry : angle 0.58762 (44432) hydrogen bonds : bond 0.04880 ( 1394) hydrogen bonds : angle 4.43482 ( 3783) *********************** 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 160 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.846 Fit side-chains REVERT: A 285 MET cc_start: 0.8784 (mmp) cc_final: 0.8012 (mtm) REVERT: A 372 ASN cc_start: 0.7770 (m-40) cc_final: 0.7471 (m110) REVERT: B 285 MET cc_start: 0.8793 (mmp) cc_final: 0.8013 (mtm) REVERT: B 372 ASN cc_start: 0.7778 (m-40) cc_final: 0.7476 (m110) REVERT: C 285 MET cc_start: 0.8780 (mmp) cc_final: 0.8015 (mtm) REVERT: C 372 ASN cc_start: 0.7792 (m-40) cc_final: 0.7492 (m110) REVERT: D 285 MET cc_start: 0.8802 (mmp) cc_final: 0.8030 (mtm) REVERT: D 372 ASN cc_start: 0.7790 (m-40) cc_final: 0.7492 (m110) outliers start: 24 outliers final: 10 residues processed: 148 average time/residue: 0.6050 time to fit residues: 106.5453 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 : 1.023 ------------------------------------------------------------------------------- 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 691 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 53 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 265 optimal weight: 10.0000 chunk 333 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 chunk 215 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 255 optimal weight: 4.9990 chunk 286 optimal weight: 0.0870 chunk 38 optimal weight: 0.7980 chunk 321 optimal weight: 2.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3588 r_free = 0.3588 target = 0.084341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.055774 restraints weight = 123696.813| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.61 r_work: 0.2771 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 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 = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 32432 Z= 0.099 Angle : 0.504 11.847 44432 Z= 0.239 Chirality : 0.038 0.141 5444 Planarity : 0.003 0.039 5100 Dihedral : 8.685 112.218 9532 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.35 % Allowed : 6.19 % Favored : 93.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.14), residues: 3612 helix: 1.28 (0.12), residues: 1804 sheet: 0.59 (0.26), residues: 472 loop : 0.70 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 393 TYR 0.010 0.001 TYR A 528 PHE 0.016 0.001 PHE C 511 TRP 0.011 0.001 TRP D 275 HIS 0.003 0.000 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00226 (32432) covalent geometry : angle 0.50408 (44432) hydrogen bonds : bond 0.03627 ( 1394) hydrogen bonds : angle 4.10618 ( 3783) *********************** 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 140 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 129 time to evaluate : 1.191 Fit side-chains REVERT: A 285 MET cc_start: 0.8640 (mmp) cc_final: 0.7951 (mtm) REVERT: A 372 ASN cc_start: 0.7686 (m-40) cc_final: 0.7391 (m110) REVERT: B 285 MET cc_start: 0.8705 (mmp) cc_final: 0.7936 (mtm) REVERT: B 372 ASN cc_start: 0.7687 (m-40) cc_final: 0.7390 (m110) REVERT: C 285 MET cc_start: 0.8625 (mmp) cc_final: 0.7839 (mtm) REVERT: C 372 ASN cc_start: 0.7702 (m-40) cc_final: 0.7406 (m110) REVERT: D 285 MET cc_start: 0.8691 (mmp) cc_final: 0.7921 (mtm) REVERT: D 372 ASN cc_start: 0.7699 (m-40) cc_final: 0.7405 (m110) outliers start: 11 outliers final: 4 residues processed: 137 average time/residue: 0.6806 time to fit residues: 111.1256 Evaluate side-chains 131 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 983 LEU 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 76 optimal weight: 5.9990 chunk 259 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 274 optimal weight: 8.9990 chunk 248 optimal weight: 0.4980 chunk 128 optimal weight: 3.9990 chunk 302 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- 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 142 GLN C 328 ASN D 328 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.083193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.054463 restraints weight = 127078.950| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.64 r_work: 0.2735 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 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 = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 32432 Z= 0.156 Angle : 0.530 11.189 44432 Z= 0.254 Chirality : 0.039 0.153 5444 Planarity : 0.003 0.037 5100 Dihedral : 8.627 110.697 9532 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.44 % Allowed : 6.50 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.14), residues: 3612 helix: 1.17 (0.12), residues: 1804 sheet: 0.61 (0.26), residues: 464 loop : 0.66 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 575 TYR 0.015 0.001 TYR A1015 PHE 0.016 0.001 PHE C 511 TRP 0.011 0.001 TRP D 275 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00378 (32432) covalent geometry : angle 0.52987 (44432) hydrogen bonds : bond 0.04179 ( 1394) hydrogen bonds : angle 4.22427 ( 3783) *********************** 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 143 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 1.170 Fit side-chains REVERT: A 285 MET cc_start: 0.8685 (mmp) cc_final: 0.7956 (mtm) REVERT: A 372 ASN cc_start: 0.7706 (m-40) cc_final: 0.7412 (m110) REVERT: B 285 MET cc_start: 0.8752 (mmp) cc_final: 0.7975 (mtm) REVERT: B 372 ASN cc_start: 0.7714 (m-40) cc_final: 0.7419 (m110) REVERT: C 285 MET cc_start: 0.8699 (mmp) cc_final: 0.7875 (mtm) REVERT: C 372 ASN cc_start: 0.7729 (m-40) cc_final: 0.7435 (m110) REVERT: D 285 MET cc_start: 0.8761 (mmp) cc_final: 0.7996 (mtm) REVERT: D 372 ASN cc_start: 0.7726 (m-40) cc_final: 0.7433 (m110) outliers start: 14 outliers final: 4 residues processed: 137 average time/residue: 0.6326 time to fit residues: 103.4517 Evaluate side-chains 131 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 983 LEU 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 19 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 208 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 305 optimal weight: 0.9990 chunk 245 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 273 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.083583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.054795 restraints weight = 134679.901| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.74 r_work: 0.2738 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 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 = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2124 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= 0.130 Angle : 0.517 11.703 44432 Z= 0.247 Chirality : 0.038 0.143 5444 Planarity : 0.003 0.038 5100 Dihedral : 8.542 111.187 9532 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.38 % Allowed : 6.63 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.14), residues: 3612 helix: 1.21 (0.12), residues: 1804 sheet: 0.73 (0.27), residues: 452 loop : 0.60 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 575 TYR 0.012 0.001 TYR D1015 PHE 0.016 0.001 PHE D 511 TRP 0.011 0.001 TRP B 275 HIS 0.003 0.001 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00312 (32432) covalent geometry : angle 0.51677 (44432) hydrogen bonds : bond 0.03920 ( 1394) hydrogen bonds : angle 4.14330 ( 3783) *********************** 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 141 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 1.154 Fit side-chains REVERT: A 285 MET cc_start: 0.8638 (mmp) cc_final: 0.7929 (mtm) REVERT: A 372 ASN cc_start: 0.7689 (m-40) cc_final: 0.7392 (m110) REVERT: B 285 MET cc_start: 0.8719 (mmp) cc_final: 0.7931 (mtm) REVERT: B 372 ASN cc_start: 0.7690 (m-40) cc_final: 0.7392 (m110) REVERT: C 285 MET cc_start: 0.8665 (mmp) cc_final: 0.7842 (mtm) REVERT: C 372 ASN cc_start: 0.7712 (m-40) cc_final: 0.7395 (m110) REVERT: D 285 MET cc_start: 0.8742 (mmp) cc_final: 0.7983 (mtm) REVERT: D 372 ASN cc_start: 0.7715 (m-40) cc_final: 0.7425 (m110) outliers start: 12 outliers final: 4 residues processed: 137 average time/residue: 0.6664 time to fit residues: 108.8022 Evaluate side-chains 131 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 983 LEU 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 0 optimal weight: 20.0000 chunk 296 optimal weight: 6.9990 chunk 239 optimal weight: 9.9990 chunk 173 optimal weight: 8.9990 chunk 140 optimal weight: 0.0770 chunk 340 optimal weight: 0.0000 chunk 238 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 chunk 199 optimal weight: 2.9990 chunk 285 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 overall best weight: 1.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.084395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.055952 restraints weight = 121932.370| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.58 r_work: 0.2776 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2770 r_free = 0.2770 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 = 0.2770 r_free = 0.2770 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2127 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= 0.101 Angle : 0.496 12.227 44432 Z= 0.238 Chirality : 0.037 0.133 5444 Planarity : 0.003 0.039 5100 Dihedral : 8.300 111.181 9532 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.28 % Allowed : 6.72 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.14), residues: 3612 helix: 1.27 (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 ARG 0.005 0.000 ARG C 575 TYR 0.011 0.001 TYR A1015 PHE 0.018 0.001 PHE D 511 TRP 0.011 0.001 TRP D 275 HIS 0.002 0.000 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00233 (32432) covalent geometry : angle 0.49578 (44432) hydrogen bonds : bond 0.03585 ( 1394) hydrogen bonds : angle 4.07839 ( 3783) *********************** 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 137 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.897 Fit side-chains REVERT: A 285 MET cc_start: 0.8533 (mmp) cc_final: 0.7848 (mtm) REVERT: A 372 ASN cc_start: 0.7679 (m-40) cc_final: 0.7369 (m110) REVERT: B 285 MET cc_start: 0.8726 (mmp) cc_final: 0.7896 (mtm) REVERT: B 372 ASN cc_start: 0.7693 (m-40) cc_final: 0.7381 (m110) REVERT: C 285 MET cc_start: 0.8608 (mmp) cc_final: 0.7769 (mtm) REVERT: C 372 ASN cc_start: 0.7711 (m-40) cc_final: 0.7399 (m110) REVERT: D 285 MET cc_start: 0.8690 (mmp) cc_final: 0.7887 (mtm) REVERT: D 372 ASN cc_start: 0.7703 (m-40) cc_final: 0.7392 (m110) outliers start: 9 outliers final: 4 residues processed: 135 average time/residue: 0.6472 time to fit residues: 103.7915 Evaluate side-chains 131 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 0.974 ------------------------------------------------------------------------------- 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 983 LEU 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 261 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 289 optimal weight: 0.7980 chunk 173 optimal weight: 5.9990 chunk 344 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 95 optimal weight: 0.0470 chunk 355 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- 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 = 0.084340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.055611 restraints weight = 142423.323| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 3.82 r_work: 0.2769 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 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 = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2139 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= 0.105 Angle : 0.495 12.437 44432 Z= 0.239 Chirality : 0.038 0.133 5444 Planarity : 0.003 0.039 5100 Dihedral : 8.172 109.206 9532 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.13 % Allowed : 6.82 % Favored : 93.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.14), residues: 3612 helix: 1.30 (0.12), residues: 1804 sheet: 0.85 (0.27), residues: 452 loop : 0.63 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 575 TYR 0.011 0.001 TYR A1015 PHE 0.017 0.001 PHE B 303 TRP 0.011 0.001 TRP D 275 HIS 0.002 0.000 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00245 (32432) covalent geometry : angle 0.49523 (44432) hydrogen bonds : bond 0.03626 ( 1394) hydrogen bonds : angle 4.05975 ( 3783) ********************** 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: 4 poor density : 129 time to evaluate : 0.963 Fit side-chains REVERT: A 285 MET cc_start: 0.8537 (mmp) cc_final: 0.7838 (mtm) REVERT: A 372 ASN cc_start: 0.7732 (m-40) cc_final: 0.7410 (m110) REVERT: B 285 MET cc_start: 0.8737 (mmp) cc_final: 0.7930 (mtm) REVERT: B 372 ASN cc_start: 0.7735 (m-40) cc_final: 0.7413 (m110) REVERT: C 285 MET cc_start: 0.8596 (mmp) cc_final: 0.7765 (mtm) REVERT: C 372 ASN cc_start: 0.7737 (m-40) cc_final: 0.7415 (m110) REVERT: C 575 ARG cc_start: 0.8200 (pmt170) cc_final: 0.7912 (pmt170) REVERT: D 285 MET cc_start: 0.8732 (mmp) cc_final: 0.7924 (mtm) REVERT: D 372 ASN cc_start: 0.7741 (m-40) cc_final: 0.7421 (m110) outliers start: 4 outliers final: 4 residues processed: 133 average time/residue: 0.6946 time to fit residues: 110.0456 Evaluate side-chains 131 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 127 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 983 LEU 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 150 optimal weight: 1.9990 chunk 259 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 0.3980 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 chunk 102 optimal weight: 8.9990 chunk 118 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 142 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.084172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.055661 restraints weight = 126359.232| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 3.65 r_work: 0.2766 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 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 = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2169 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= 0.113 Angle : 0.496 12.453 44432 Z= 0.241 Chirality : 0.038 0.136 5444 Planarity : 0.003 0.038 5100 Dihedral : 8.118 106.883 9532 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.25 % Allowed : 6.72 % Favored : 93.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.14), residues: 3612 helix: 1.28 (0.12), residues: 1804 sheet: 0.84 (0.27), residues: 452 loop : 0.62 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 575 TYR 0.012 0.001 TYR B1015 PHE 0.020 0.001 PHE D 303 TRP 0.011 0.001 TRP C 275 HIS 0.002 0.000 HIS D 254 Details of bonding type rmsd covalent geometry : bond 0.00266 (32432) covalent geometry : angle 0.49612 (44432) hydrogen bonds : bond 0.03695 ( 1394) hydrogen bonds : angle 4.06072 ( 3783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10265.09 seconds wall clock time: 175 minutes 35.18 seconds (10535.18 seconds total)