Starting phenix.real_space_refine on Mon Jul 6 01:01:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v64_42989/07_2026/8v64_42989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v64_42989/07_2026/8v64_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_42989/07_2026/8v64_42989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v64_42989/07_2026/8v64_42989.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v64_42989/07_2026/8v64_42989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v64_42989/07_2026/8v64_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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, 668 Ad-hoc single atom residues: {' K': 6} Unusual residues: {'AJP': 9, 'CLR': 1, 'POV': 7} Classifications: {'undetermined': 17} Link IDs: {None: 16} Chain breaks: 6 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, 631 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'AJP': 9, 'CLR': 1, 'POV': 6} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain breaks: 1 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, 631 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'AJP': 9, 'CLR': 1, 'POV': 6} Classifications: {'undetermined': 16} Link IDs: {None: 15} Chain breaks: 1 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, 594 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'AJP': 9, 'CLR': 1, 'POV': 5} Classifications: {'undetermined': 15} Link IDs: {None: 14} Chain breaks: 1 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: 11.47, per 1000 atoms: 0.36 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: 2.68 Conformation dependent library (CDL) restraints added in 1.7 seconds 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 24 sheets defined 54.8% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 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: 7.04 Time building geometry restraints manager: 3.56 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: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 35.160 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.100 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:8.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 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 are 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/Z covalent geometry : bond 0.00429 / 0.21 (32432) covalent geometry : angle 0.64685 / 0.28 (44432) hydrogen bonds : bond 0.16188 / 10.46 ( 1394) hydrogen bonds : angle 5.48814 / 3.86 ( 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 : 1.175 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: 0.8570 (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: 0.6939 time to fit residues: 155.1072 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 : 1.201 ------------------------------------------------------------------------------- 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... 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 328 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.085131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.056837 restraints weight = 104874.737| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.39 r_work: 0.2816 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2808 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2808 r_free = 0.2808 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 = 0.2808 r_free = 0.2808 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2808 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 32432 Z= 0.139 Angle : 0.675 8.662 44432 Z= 0.296 Chirality : 0.043 0.253 5444 Planarity : 0.004 0.043 5100 Dihedral : 15.532 123.991 9532 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.38 % Allowed : 3.36 % 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 are not related in a simple way. whole: 1.02 (0.14), residues: 3612 helix: 0.92 (0.12), residues: 1800 sheet: 0.41 (0.26), residues: 464 loop : 0.71 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 393 TYR 0.021 0.001 TYR A1015 PHE 0.024 0.002 PHE D 303 TRP 0.013 0.001 TRP A 100 HIS 0.003 0.001 HIS A 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (32432) covalent geometry : angle 0.67495 / 0.30 (44432) hydrogen bonds : bond 0.03973 / 2.57 ( 1394) hydrogen bonds : angle 4.38728 / 3.06 ( 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 152 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.783 Fit side-chains REVERT: A 154 MET cc_start: 0.8962 (mtm) cc_final: 0.8643 (mtm) REVERT: A 285 MET cc_start: 0.8509 (mmp) cc_final: 0.7855 (mtm) REVERT: B 154 MET cc_start: 0.8949 (mtm) cc_final: 0.8650 (mtm) REVERT: B 285 MET cc_start: 0.8478 (mmp) cc_final: 0.7713 (mtm) REVERT: C 154 MET cc_start: 0.8977 (mtm) cc_final: 0.8662 (mtm) REVERT: C 285 MET cc_start: 0.8486 (mmp) cc_final: 0.7717 (mtm) REVERT: D 154 MET cc_start: 0.8976 (mtm) cc_final: 0.8660 (mtm) REVERT: D 285 MET cc_start: 0.8459 (mmp) cc_final: 0.7708 (mtm) outliers start: 12 outliers final: 4 residues processed: 148 average time/residue: 0.6698 time to fit residues: 117.4528 Evaluate side-chains 125 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 121 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 297 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 315 optimal weight: 8.9990 chunk 247 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 343 optimal weight: 10.0000 chunk 224 optimal weight: 8.9990 chunk 210 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 304 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 GLN A 328 ASN B 328 ASN C 142 GLN C 328 ASN D 142 GLN D 328 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.082806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.054091 restraints weight = 119081.954| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.55 r_work: 0.2730 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 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 = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 32432 Z= 0.208 Angle : 0.654 10.182 44432 Z= 0.299 Chirality : 0.043 0.296 5444 Planarity : 0.004 0.056 5100 Dihedral : 11.199 116.542 9532 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.75 % Allowed : 3.99 % Favored : 95.26 % 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 are not related in a simple way. whole: 0.96 (0.14), residues: 3612 helix: 0.90 (0.12), residues: 1800 sheet: 0.26 (0.26), residues: 476 loop : 0.68 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 393 TYR 0.023 0.002 TYR D1015 PHE 0.034 0.002 PHE C 303 TRP 0.013 0.001 TRP D 275 HIS 0.005 0.001 HIS C 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00501 / 0.21 (32432) covalent geometry : angle 0.65405 / 0.30 (44432) hydrogen bonds : bond 0.04982 / 3.24 ( 1394) hydrogen bonds : angle 4.48275 / 3.13 ( 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 148 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.168 Fit side-chains REVERT: A 154 MET cc_start: 0.8884 (mtm) cc_final: 0.8591 (mtm) REVERT: A 285 MET cc_start: 0.8743 (mmp) cc_final: 0.7948 (mtm) REVERT: A 372 ASN cc_start: 0.7826 (m-40) cc_final: 0.7509 (m110) REVERT: B 154 MET cc_start: 0.8872 (mtm) cc_final: 0.8599 (mtm) REVERT: B 285 MET cc_start: 0.8666 (mmp) cc_final: 0.7869 (mtm) REVERT: C 154 MET cc_start: 0.8868 (mtm) cc_final: 0.8582 (mtm) REVERT: C 285 MET cc_start: 0.8664 (mmp) cc_final: 0.7865 (mtm) REVERT: D 154 MET cc_start: 0.8874 (mtm) cc_final: 0.8590 (mtm) REVERT: D 285 MET cc_start: 0.8695 (mmp) cc_final: 0.7871 (mtm) REVERT: D 372 ASN cc_start: 0.7845 (m-40) cc_final: 0.7529 (m110) outliers start: 24 outliers final: 8 residues processed: 136 average time/residue: 0.6253 time to fit residues: 102.0462 Evaluate side-chains 132 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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: 10.0000 chunk 190 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 7 optimal weight: 0.1980 chunk 317 optimal weight: 4.9990 chunk 291 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 320 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3593 r_free = 0.3593 target = 0.084382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.055882 restraints weight = 125436.249| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 3.62 r_work: 0.2776 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 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 = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 32432 Z= 0.117 Angle : 0.531 10.224 44432 Z= 0.247 Chirality : 0.039 0.210 5444 Planarity : 0.003 0.040 5100 Dihedral : 9.518 115.097 9532 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.47 % Allowed : 5.28 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.14), residues: 3612 helix: 1.19 (0.12), residues: 1800 sheet: 0.44 (0.26), residues: 472 loop : 0.72 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 393 TYR 0.012 0.001 TYR A1015 PHE 0.017 0.001 PHE C 303 TRP 0.010 0.001 TRP D 275 HIS 0.002 0.000 HIS B 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (32432) covalent geometry : angle 0.53050 / 0.25 (44432) hydrogen bonds : bond 0.03729 / 2.41 ( 1394) hydrogen bonds : angle 4.15971 / 2.90 ( 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 148 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.815 Fit side-chains REVERT: A 285 MET cc_start: 0.8597 (mmp) cc_final: 0.7886 (mtm) REVERT: A 372 ASN cc_start: 0.7754 (m-40) cc_final: 0.7460 (m110) REVERT: B 285 MET cc_start: 0.8530 (mmp) cc_final: 0.7709 (mtm) REVERT: B 372 ASN cc_start: 0.7757 (m-40) cc_final: 0.7462 (m110) REVERT: C 285 MET cc_start: 0.8555 (mmp) cc_final: 0.7743 (mtm) REVERT: C 372 ASN cc_start: 0.7769 (m-40) cc_final: 0.7475 (m110) REVERT: D 285 MET cc_start: 0.8553 (mmp) cc_final: 0.7712 (mtm) REVERT: D 372 ASN cc_start: 0.7773 (m-40) cc_final: 0.7481 (m110) outliers start: 15 outliers final: 8 residues processed: 145 average time/residue: 0.6011 time to fit residues: 104.3689 Evaluate side-chains 137 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 129 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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: 0.9990 chunk 178 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 142 optimal weight: 0.2980 chunk 262 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 231 optimal weight: 8.9990 chunk 281 optimal weight: 6.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 ASN A 957 ASN B 142 GLN B 328 ASN B 957 ASN C 328 ASN C 957 ASN D 328 ASN D 957 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.083027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.054328 restraints weight = 121110.559| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.57 r_work: 0.2733 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 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 = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 32432 Z= 0.166 Angle : 0.553 10.693 44432 Z= 0.262 Chirality : 0.040 0.155 5444 Planarity : 0.004 0.038 5100 Dihedral : 8.906 107.584 9532 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.63 % Allowed : 5.75 % Favored : 93.62 % 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 are not related in a simple way. whole: 1.23 (0.14), residues: 3612 helix: 1.16 (0.12), residues: 1800 sheet: 0.44 (0.26), residues: 472 loop : 0.72 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 393 TYR 0.016 0.001 TYR B1015 PHE 0.019 0.001 PHE A 303 TRP 0.011 0.001 TRP C 275 HIS 0.003 0.001 HIS C 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (32432) covalent geometry : angle 0.55339 / 0.26 (44432) hydrogen bonds : bond 0.04305 / 2.80 ( 1394) hydrogen bonds : angle 4.26739 / 2.98 ( 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 153 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.193 Fit side-chains REVERT: A 285 MET cc_start: 0.8682 (mmp) cc_final: 0.7851 (mtm) REVERT: A 372 ASN cc_start: 0.7727 (m-40) cc_final: 0.7381 (m110) REVERT: B 285 MET cc_start: 0.8641 (mmp) cc_final: 0.7827 (mtm) REVERT: B 372 ASN cc_start: 0.7731 (m-40) cc_final: 0.7384 (m110) REVERT: C 285 MET cc_start: 0.8637 (mmp) cc_final: 0.7822 (mtm) REVERT: C 372 ASN cc_start: 0.7745 (m-40) cc_final: 0.7415 (m110) REVERT: D 285 MET cc_start: 0.8656 (mmp) cc_final: 0.7824 (mtm) REVERT: D 372 ASN cc_start: 0.7746 (m-40) cc_final: 0.7404 (m110) outliers start: 20 outliers final: 8 residues processed: 145 average time/residue: 0.6065 time to fit residues: 105.2547 Evaluate side-chains 134 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 53 optimal weight: 0.0970 chunk 118 optimal weight: 2.9990 chunk 265 optimal weight: 4.9990 chunk 333 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 286 optimal weight: 0.0020 chunk 38 optimal weight: 2.9990 chunk 321 optimal weight: 4.9990 overall best weight: 2.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3584 r_free = 0.3584 target = 0.083921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.055370 restraints weight = 123577.243| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.61 r_work: 0.2756 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2760 r_free = 0.2760 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 = 0.2760 r_free = 0.2760 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 32432 Z= 0.120 Angle : 0.511 10.911 44432 Z= 0.243 Chirality : 0.038 0.142 5444 Planarity : 0.003 0.039 5100 Dihedral : 8.694 111.172 9532 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.50 % Allowed : 6.16 % Favored : 93.34 % 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 are not related in a simple way. whole: 1.35 (0.14), residues: 3612 helix: 1.26 (0.12), residues: 1804 sheet: 0.52 (0.26), residues: 472 loop : 0.75 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 393 TYR 0.012 0.001 TYR B1015 PHE 0.016 0.001 PHE D 511 TRP 0.010 0.001 TRP D 275 HIS 0.002 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (32432) covalent geometry : angle 0.51129 / 0.24 (44432) hydrogen bonds : bond 0.03795 / 2.46 ( 1394) hydrogen bonds : angle 4.12384 / 2.88 ( 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 144 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 1.222 Fit side-chains REVERT: A 285 MET cc_start: 0.8612 (mmp) cc_final: 0.7896 (mtm) REVERT: A 372 ASN cc_start: 0.7698 (m-40) cc_final: 0.7364 (m110) REVERT: B 285 MET cc_start: 0.8574 (mmp) cc_final: 0.7766 (mtm) REVERT: B 372 ASN cc_start: 0.7693 (m-40) cc_final: 0.7357 (m110) REVERT: C 285 MET cc_start: 0.8563 (mmp) cc_final: 0.7754 (mtm) REVERT: C 372 ASN cc_start: 0.7709 (m-40) cc_final: 0.7378 (m110) REVERT: D 285 MET cc_start: 0.8599 (mmp) cc_final: 0.7755 (mtm) REVERT: D 372 ASN cc_start: 0.7707 (m-40) cc_final: 0.7376 (m110) outliers start: 16 outliers final: 4 residues processed: 136 average time/residue: 0.6636 time to fit residues: 107.7993 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 : 1.137 ------------------------------------------------------------------------------- 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: 2.9990 chunk 259 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 274 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 302 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3571 r_free = 0.3571 target = 0.083200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.054561 restraints weight = 127060.456| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 3.63 r_work: 0.2741 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 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 = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 32432 Z= 0.154 Angle : 0.535 12.050 44432 Z= 0.254 Chirality : 0.039 0.152 5444 Planarity : 0.003 0.037 5100 Dihedral : 8.621 110.514 9532 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.60 % Allowed : 6.34 % 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 are not related in a simple way. whole: 1.32 (0.14), residues: 3612 helix: 1.23 (0.12), residues: 1804 sheet: 0.53 (0.26), residues: 472 loop : 0.74 (0.17), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 575 TYR 0.014 0.001 TYR D1015 PHE 0.015 0.001 PHE D 511 TRP 0.011 0.001 TRP D 275 HIS 0.003 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 (32432) covalent geometry : angle 0.53456 / 0.25 (44432) hydrogen bonds : bond 0.04149 / 2.69 ( 1394) hydrogen bonds : angle 4.19953 / 2.94 ( 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 152 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.222 Fit side-chains REVERT: A 285 MET cc_start: 0.8677 (mmp) cc_final: 0.7848 (mtm) REVERT: A 372 ASN cc_start: 0.7696 (m-40) cc_final: 0.7378 (m110) REVERT: A 1009 MET cc_start: 0.8967 (ttp) cc_final: 0.8701 (ttp) REVERT: B 285 MET cc_start: 0.8639 (mmp) cc_final: 0.7801 (mtm) REVERT: B 372 ASN cc_start: 0.7690 (m-40) cc_final: 0.7385 (m110) REVERT: B 1009 MET cc_start: 0.8960 (ttp) cc_final: 0.8694 (ttp) REVERT: C 285 MET cc_start: 0.8623 (mmp) cc_final: 0.7791 (mtm) REVERT: C 372 ASN cc_start: 0.7705 (m-40) cc_final: 0.7404 (m110) REVERT: C 1009 MET cc_start: 0.8960 (ttp) cc_final: 0.8692 (ttp) REVERT: D 285 MET cc_start: 0.8637 (mmp) cc_final: 0.7798 (mtm) REVERT: D 372 ASN cc_start: 0.7703 (m-40) cc_final: 0.7403 (m110) REVERT: D 1009 MET cc_start: 0.8963 (ttp) cc_final: 0.8699 (ttp) outliers start: 19 outliers final: 8 residues processed: 145 average time/residue: 0.6424 time to fit residues: 111.7627 Evaluate side-chains 135 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 19 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 208 optimal weight: 7.9990 chunk 169 optimal weight: 0.3980 chunk 305 optimal weight: 7.9990 chunk 245 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 273 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 99 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3590 r_free = 0.3590 target = 0.084190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.055553 restraints weight = 134897.588| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.73 r_work: 0.2764 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 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 = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32432 Z= 0.107 Angle : 0.507 13.065 44432 Z= 0.240 Chirality : 0.038 0.135 5444 Planarity : 0.003 0.039 5100 Dihedral : 8.463 111.441 9532 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.44 % Allowed : 6.60 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.14), residues: 3612 helix: 1.41 (0.12), residues: 1768 sheet: 0.66 (0.26), residues: 472 loop : 0.79 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 575 TYR 0.011 0.001 TYR A1015 PHE 0.017 0.001 PHE D 511 TRP 0.011 0.001 TRP D 275 HIS 0.002 0.000 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (32432) covalent geometry : angle 0.50692 / 0.24 (44432) hydrogen bonds : bond 0.03646 / 2.35 ( 1394) hydrogen bonds : angle 4.05534 / 2.83 ( 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: 14 poor density : 127 time to evaluate : 1.182 Fit side-chains REVERT: A 285 MET cc_start: 0.8584 (mmp) cc_final: 0.7866 (mtm) REVERT: A 372 ASN cc_start: 0.7664 (m-40) cc_final: 0.7341 (m110) REVERT: A 1009 MET cc_start: 0.8854 (ttp) cc_final: 0.8527 (ttp) REVERT: B 285 MET cc_start: 0.8562 (mmp) cc_final: 0.7718 (mtm) REVERT: B 372 ASN cc_start: 0.7660 (m-40) cc_final: 0.7335 (m110) REVERT: B 1009 MET cc_start: 0.8847 (ttp) cc_final: 0.8518 (ttp) REVERT: C 285 MET cc_start: 0.8558 (mmp) cc_final: 0.7710 (mtm) REVERT: C 372 ASN cc_start: 0.7666 (m-40) cc_final: 0.7357 (m110) REVERT: C 1009 MET cc_start: 0.8855 (ttp) cc_final: 0.8528 (ttp) REVERT: D 285 MET cc_start: 0.8567 (mmp) cc_final: 0.7724 (mtm) REVERT: D 372 ASN cc_start: 0.7676 (m-40) cc_final: 0.7353 (m110) REVERT: D 1009 MET cc_start: 0.8850 (ttp) cc_final: 0.8522 (ttp) outliers start: 14 outliers final: 9 residues processed: 139 average time/residue: 0.6551 time to fit residues: 108.9298 Evaluate side-chains 136 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 127 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 924 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 0 optimal weight: 20.0000 chunk 296 optimal weight: 4.9990 chunk 239 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 340 optimal weight: 3.9990 chunk 238 optimal weight: 40.0000 chunk 62 optimal weight: 0.9980 chunk 199 optimal weight: 1.9990 chunk 285 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 ASN B 328 ASN C 328 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.083836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.055284 restraints weight = 121923.002| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.61 r_work: 0.2769 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 32432 Z= 0.123 Angle : 0.513 13.123 44432 Z= 0.246 Chirality : 0.038 0.142 5444 Planarity : 0.003 0.038 5100 Dihedral : 8.312 110.344 9532 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.47 % Allowed : 6.53 % 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 are not related in a simple way. whole: 1.46 (0.14), residues: 3612 helix: 1.34 (0.12), residues: 1768 sheet: 0.68 (0.26), residues: 472 loop : 0.81 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 575 TYR 0.012 0.001 TYR A1015 PHE 0.016 0.001 PHE D 511 TRP 0.011 0.001 TRP D 275 HIS 0.002 0.001 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (32432) covalent geometry : angle 0.51256 / 0.25 (44432) hydrogen bonds : bond 0.03799 / 2.46 ( 1394) hydrogen bonds : angle 4.10337 / 2.87 ( 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 141 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.306 Fit side-chains REVERT: A 285 MET cc_start: 0.8572 (mmp) cc_final: 0.7855 (mtm) REVERT: A 372 ASN cc_start: 0.7725 (m-40) cc_final: 0.7428 (m110) REVERT: A 1009 MET cc_start: 0.8876 (ttp) cc_final: 0.8618 (ttp) REVERT: B 285 MET cc_start: 0.8604 (mmp) cc_final: 0.7763 (mtm) REVERT: B 372 ASN cc_start: 0.7729 (m-40) cc_final: 0.7417 (m110) REVERT: B 1009 MET cc_start: 0.8869 (ttp) cc_final: 0.8608 (ttp) REVERT: C 285 MET cc_start: 0.8601 (mmp) cc_final: 0.7761 (mtm) REVERT: C 372 ASN cc_start: 0.7709 (m-40) cc_final: 0.7422 (m110) REVERT: C 1009 MET cc_start: 0.8878 (ttp) cc_final: 0.8622 (ttp) REVERT: D 285 MET cc_start: 0.8616 (mmp) cc_final: 0.7777 (mtm) REVERT: D 372 ASN cc_start: 0.7740 (m-40) cc_final: 0.7444 (m110) REVERT: D 1009 MET cc_start: 0.8869 (ttp) cc_final: 0.8611 (ttp) outliers start: 15 outliers final: 9 residues processed: 137 average time/residue: 0.6596 time to fit residues: 108.3000 Evaluate side-chains 135 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 924 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 261 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 289 optimal weight: 0.6980 chunk 173 optimal weight: 7.9990 chunk 344 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 355 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 235 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.082630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.053698 restraints weight = 142234.859| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.81 r_work: 0.2713 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2713 r_free = 0.2713 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 = 0.2713 r_free = 0.2713 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 32432 Z= 0.189 Angle : 0.559 12.471 44432 Z= 0.269 Chirality : 0.040 0.161 5444 Planarity : 0.004 0.037 5100 Dihedral : 8.384 107.721 9532 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.41 % Allowed : 6.56 % 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 are not related in a simple way. whole: 1.12 (0.14), residues: 3612 helix: 1.02 (0.12), residues: 1808 sheet: 0.74 (0.27), residues: 448 loop : 0.58 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 575 TYR 0.013 0.001 TYR D1015 PHE 0.014 0.001 PHE D 511 TRP 0.011 0.001 TRP D 275 HIS 0.003 0.001 HIS C 350 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.19 (32432) covalent geometry : angle 0.55941 / 0.27 (44432) hydrogen bonds : bond 0.04448 / 2.89 ( 1394) hydrogen bonds : angle 4.28193 / 3.00 ( 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 142 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 129 time to evaluate : 1.165 Fit side-chains REVERT: A 285 MET cc_start: 0.8704 (mmp) cc_final: 0.7895 (mtp) REVERT: A 372 ASN cc_start: 0.7715 (m-40) cc_final: 0.7397 (m110) REVERT: A 1009 MET cc_start: 0.8984 (ttp) cc_final: 0.8756 (ttp) REVERT: B 285 MET cc_start: 0.8695 (mmp) cc_final: 0.7921 (mtm) REVERT: B 372 ASN cc_start: 0.7714 (m-40) cc_final: 0.7401 (m110) REVERT: B 1009 MET cc_start: 0.8980 (ttp) cc_final: 0.8751 (ttp) REVERT: C 285 MET cc_start: 0.8692 (mmp) cc_final: 0.7917 (mtm) REVERT: C 372 ASN cc_start: 0.7730 (m-40) cc_final: 0.7414 (m110) REVERT: C 1009 MET cc_start: 0.8984 (ttp) cc_final: 0.8757 (ttp) REVERT: D 285 MET cc_start: 0.8696 (mmp) cc_final: 0.7916 (mtm) REVERT: D 372 ASN cc_start: 0.7730 (m-40) cc_final: 0.7420 (m110) REVERT: D 1009 MET cc_start: 0.8982 (ttp) cc_final: 0.8756 (ttp) outliers start: 13 outliers final: 8 residues processed: 137 average time/residue: 0.6421 time to fit residues: 105.3864 Evaluate side-chains 134 residues out of total 3180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 364 random chunks: chunk 150 optimal weight: 4.9990 chunk 259 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 102 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.084237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.055775 restraints weight = 126020.296| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.63 r_work: 0.2781 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 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 = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 32432 Z= 0.102 Angle : 0.500 12.331 44432 Z= 0.242 Chirality : 0.038 0.135 5444 Planarity : 0.003 0.039 5100 Dihedral : 8.233 108.715 9532 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.35 % Allowed : 6.66 % 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 are not related in a simple way. whole: 1.45 (0.14), residues: 3612 helix: 1.34 (0.12), residues: 1768 sheet: 0.68 (0.27), residues: 472 loop : 0.78 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 575 TYR 0.010 0.001 TYR D1015 PHE 0.016 0.001 PHE B 511 TRP 0.011 0.001 TRP D 275 HIS 0.002 0.000 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (32432) covalent geometry : angle 0.49998 / 0.24 (44432) hydrogen bonds : bond 0.03615 / 2.33 ( 1394) hydrogen bonds : angle 4.07784 / 2.85 ( 3783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10758.02 seconds wall clock time: 184 minutes 5.58 seconds (11045.58 seconds total)