Starting phenix.real_space_refine on Thu Feb 5 17:59:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qdn_53031/02_2026/9qdn_53031.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qdn_53031/02_2026/9qdn_53031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qdn_53031/02_2026/9qdn_53031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qdn_53031/02_2026/9qdn_53031.map" model { file = "/net/cci-nas-00/data/ceres_data/9qdn_53031/02_2026/9qdn_53031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qdn_53031/02_2026/9qdn_53031.cif" } resolution = 2.71 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= 0.001 sd= 0.056 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 12340 2.51 5 N 2978 2.21 5 O 3361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18807 Number of models: 1 Model: "" Number of chains: 20 Chain: "H" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1393 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 178} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 3173 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 405, 3165 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 405, 3165 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3229 Chain: "A" Number of atoms: 3145 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3137 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 401, 3137 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3201 Chain: "G" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1447 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "E" Number of atoms: 1447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1447 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 3145 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3137 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 401, 3137 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3201 Chain: "B" Number of atoms: 3173 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 405, 3165 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 405, 3165 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 388} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 3229 Chain: "F" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1393 Classifications: {'peptide': 181} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 178} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'PLM': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 101 Unusual residues: {'E2Q': 1, 'OLC': 1, 'PLM': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Unusual residues: {'E2Q': 1, 'OLC': 1, 'PLM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 101 Unusual residues: {'E2Q': 1, 'OLC': 1, 'PLM': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 119 Unusual residues: {'E2Q': 1, 'OLC': 1, 'PLM': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 5.95, per 1000 atoms: 0.32 Number of scatterers: 18807 At special positions: 0 Unit cell: (128.594, 110.5, 142.164, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 3361 8.00 N 2978 7.00 C 12340 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.03 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Simple disulfide: pdb=" SG CYS D 611 " - pdb=" SG CYS A 611 " distance=2.02 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 795 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.03 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.03 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 611 " - pdb=" SG CYS B 611 " distance=2.05 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 795 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 795 " distance=2.03 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.03 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 981.1 milliseconds 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4336 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 28 sheets defined 59.3% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'H' and resid 7 through 30 Processing helix chain 'H' and resid 92 through 105 removed outlier: 4.251A pdb=" N LEU H 98 " --> pdb=" O ALA H 94 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG H 99 " --> pdb=" O GLU H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 128 removed outlier: 3.578A pdb=" N PHE H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 160 removed outlier: 3.638A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 212 removed outlier: 3.510A pdb=" N ILE H 188 " --> pdb=" O ALA H 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 removed outlier: 3.659A pdb=" N TYR D 443 " --> pdb=" O ASN D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 457 removed outlier: 3.813A pdb=" N ALA D 451 " --> pdb=" O CYS D 447 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER D 452 " --> pdb=" O VAL D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 491 removed outlier: 3.553A pdb=" N LEU D 489 " --> pdb=" O MET D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 509 Processing helix chain 'D' and resid 537 through 541 Processing helix chain 'D' and resid 544 through 568 Processing helix chain 'D' and resid 594 through 607 Processing helix chain 'D' and resid 617 through 648 Processing helix chain 'D' and resid 657 through 664 removed outlier: 3.869A pdb=" N GLN D 664 " --> pdb=" O ASP D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 676 through 684 removed outlier: 3.588A pdb=" N PHE D 681 " --> pdb=" O THR D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 698 removed outlier: 3.525A pdb=" N TYR D 695 " --> pdb=" O LYS D 691 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER D 698 " --> pdb=" O THR D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 718 Processing helix chain 'D' and resid 728 through 732 Processing helix chain 'D' and resid 733 through 737 Processing helix chain 'D' and resid 764 through 779 Processing helix chain 'D' and resid 779 through 790 removed outlier: 3.524A pdb=" N LYS D 785 " --> pdb=" O LEU D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 843 removed outlier: 3.598A pdb=" N PHE D 818 " --> pdb=" O VAL D 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 438 through 441 removed outlier: 4.167A pdb=" N ASP A 441 " --> pdb=" O GLU A 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 441' Processing helix chain 'A' and resid 445 through 459 Processing helix chain 'A' and resid 485 through 491 Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 537 through 541 removed outlier: 3.791A pdb=" N LEU A 540 " --> pdb=" O PHE A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 568 removed outlier: 3.515A pdb=" N PHE A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 607 Processing helix chain 'A' and resid 617 through 652 Processing helix chain 'A' and resid 657 through 664 removed outlier: 3.761A pdb=" N LEU A 661 " --> pdb=" O SER A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 removed outlier: 3.604A pdb=" N GLU A 679 " --> pdb=" O GLY A 675 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE A 681 " --> pdb=" O THR A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 699 removed outlier: 4.457A pdb=" N MET A 692 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER A 698 " --> pdb=" O THR A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 717 removed outlier: 3.751A pdb=" N ARG A 716 " --> pdb=" O VAL A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 735 Processing helix chain 'A' and resid 764 through 778 removed outlier: 3.646A pdb=" N SER A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 790 Processing helix chain 'A' and resid 810 through 813 Processing helix chain 'A' and resid 814 through 843 removed outlier: 3.508A pdb=" N PHE A 818 " --> pdb=" O VAL A 814 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 30 removed outlier: 3.946A pdb=" N LEU G 12 " --> pdb=" O VAL G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 105 removed outlier: 3.530A pdb=" N SER G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 128 removed outlier: 3.708A pdb=" N VAL G 112 " --> pdb=" O PRO G 108 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR G 128 " --> pdb=" O ALA G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 161 removed outlier: 3.794A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA G 161 " --> pdb=" O ILE G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 214 removed outlier: 3.629A pdb=" N GLY G 183 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 208 " --> pdb=" O ARG G 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG G 209 " --> pdb=" O HIS G 205 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA G 210 " --> pdb=" O LYS G 206 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR G 211 " --> pdb=" O GLN G 207 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA G 212 " --> pdb=" O LEU G 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 30 removed outlier: 3.946A pdb=" N LEU E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 105 removed outlier: 3.529A pdb=" N SER E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 removed outlier: 3.708A pdb=" N VAL E 112 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU E 126 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR E 128 " --> pdb=" O ALA E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 161 removed outlier: 3.795A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA E 161 " --> pdb=" O ILE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 214 removed outlier: 3.628A pdb=" N GLY E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 208 " --> pdb=" O ARG E 204 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG E 209 " --> pdb=" O HIS E 205 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA E 210 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 437 Processing helix chain 'C' and resid 438 through 441 removed outlier: 4.167A pdb=" N ASP C 441 " --> pdb=" O GLU C 438 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 445 through 459 Processing helix chain 'C' and resid 485 through 491 Processing helix chain 'C' and resid 504 through 509 Processing helix chain 'C' and resid 537 through 541 removed outlier: 3.791A pdb=" N LEU C 540 " --> pdb=" O PHE C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 568 removed outlier: 3.515A pdb=" N PHE C 568 " --> pdb=" O LEU C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 607 Processing helix chain 'C' and resid 617 through 652 Processing helix chain 'C' and resid 657 through 664 removed outlier: 3.760A pdb=" N LEU C 661 " --> pdb=" O SER C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 684 removed outlier: 3.605A pdb=" N GLU C 679 " --> pdb=" O GLY C 675 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE C 681 " --> pdb=" O THR C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 699 removed outlier: 4.458A pdb=" N MET C 692 " --> pdb=" O VAL C 688 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER C 698 " --> pdb=" O THR C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 717 removed outlier: 3.751A pdb=" N ARG C 716 " --> pdb=" O VAL C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 735 Processing helix chain 'C' and resid 764 through 778 removed outlier: 3.646A pdb=" N SER C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 790 Processing helix chain 'C' and resid 810 through 813 Processing helix chain 'C' and resid 814 through 843 removed outlier: 3.509A pdb=" N PHE C 818 " --> pdb=" O VAL C 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.658A pdb=" N TYR B 443 " --> pdb=" O ASN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 457 removed outlier: 3.813A pdb=" N ALA B 451 " --> pdb=" O CYS B 447 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 491 removed outlier: 3.552A pdb=" N LEU B 489 " --> pdb=" O MET B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 509 Processing helix chain 'B' and resid 537 through 541 Processing helix chain 'B' and resid 544 through 568 Processing helix chain 'B' and resid 594 through 607 Processing helix chain 'B' and resid 617 through 648 Processing helix chain 'B' and resid 657 through 664 removed outlier: 3.867A pdb=" N GLN B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 676 through 684 removed outlier: 3.589A pdb=" N PHE B 681 " --> pdb=" O THR B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 698 removed outlier: 3.525A pdb=" N TYR B 695 " --> pdb=" O LYS B 691 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER B 698 " --> pdb=" O THR B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 718 Processing helix chain 'B' and resid 728 through 732 Processing helix chain 'B' and resid 733 through 737 Processing helix chain 'B' and resid 764 through 779 Processing helix chain 'B' and resid 779 through 790 removed outlier: 3.524A pdb=" N LYS B 785 " --> pdb=" O LEU B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 843 removed outlier: 3.598A pdb=" N PHE B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 30 Processing helix chain 'F' and resid 92 through 105 removed outlier: 4.250A pdb=" N LEU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG F 99 " --> pdb=" O GLU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 128 removed outlier: 3.578A pdb=" N PHE F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 160 removed outlier: 3.639A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 212 removed outlier: 3.509A pdb=" N ILE F 188 " --> pdb=" O ALA F 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 77 through 79 Processing sheet with id=AA2, first strand: chain 'D' and resid 417 through 419 removed outlier: 6.370A pdb=" N VAL D 417 " --> pdb=" O LYS D 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 474 through 475 removed outlier: 3.732A pdb=" N ALA D 474 " --> pdb=" O ASN D 483 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 497 through 502 removed outlier: 3.908A pdb=" N ALA D 757 " --> pdb=" O ALA D 497 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA D 499 " --> pdb=" O GLY D 755 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY D 755 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU D 501 " --> pdb=" O GLY D 753 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY D 753 " --> pdb=" O LEU D 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 497 through 502 removed outlier: 3.908A pdb=" N ALA D 757 " --> pdb=" O ALA D 497 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ALA D 499 " --> pdb=" O GLY D 755 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY D 755 " --> pdb=" O ALA D 499 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU D 501 " --> pdb=" O GLY D 753 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY D 753 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET D 518 " --> pdb=" O TYR D 754 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 668 through 670 removed outlier: 6.736A pdb=" N ALA D 668 " --> pdb=" O ALA D 723 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N LEU D 725 " --> pdb=" O ALA D 668 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLY D 670 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N GLU D 727 " --> pdb=" O GLY D 670 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N PHE D 722 " --> pdb=" O LYS D 527 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LYS D 527 " --> pdb=" O PHE D 722 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE D 524 " --> pdb=" O VAL D 745 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 420 through 421 Processing sheet with id=AA8, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 475 Processing sheet with id=AB1, first strand: chain 'A' and resid 512 through 513 removed outlier: 3.590A pdb=" N ASP A 512 " --> pdb=" O THR A 758 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 758 " --> pdb=" O ASP A 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 518 through 520 removed outlier: 3.886A pdb=" N MET A 518 " --> pdb=" O TYR A 754 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 668 through 670 removed outlier: 8.008A pdb=" N PHE A 722 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS A 527 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ILE A 524 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 526 " --> pdb=" O MET A 743 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=AB5, first strand: chain 'G' and resid 37 through 38 removed outlier: 3.591A pdb=" N HIS G 60 " --> pdb=" O CYS G 67 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS G 67 " --> pdb=" O HIS G 60 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AB7, first strand: chain 'E' and resid 37 through 38 removed outlier: 3.592A pdb=" N HIS E 60 " --> pdb=" O CYS E 67 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N CYS E 67 " --> pdb=" O HIS E 60 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 420 through 421 Processing sheet with id=AB9, first strand: chain 'C' and resid 429 through 430 Processing sheet with id=AC1, first strand: chain 'C' and resid 473 through 475 Processing sheet with id=AC2, first strand: chain 'C' and resid 512 through 513 removed outlier: 3.590A pdb=" N ASP C 512 " --> pdb=" O THR C 758 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C 758 " --> pdb=" O ASP C 512 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 518 through 520 removed outlier: 3.886A pdb=" N MET C 518 " --> pdb=" O TYR C 754 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 668 through 670 removed outlier: 8.008A pdb=" N PHE C 722 " --> pdb=" O LYS C 527 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LYS C 527 " --> pdb=" O PHE C 722 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE C 524 " --> pdb=" O VAL C 745 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 526 " --> pdb=" O MET C 743 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 417 through 419 removed outlier: 6.373A pdb=" N VAL B 417 " --> pdb=" O LYS B 463 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 474 through 475 removed outlier: 3.732A pdb=" N ALA B 474 " --> pdb=" O ASN B 483 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 497 through 502 removed outlier: 3.908A pdb=" N ALA B 757 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA B 499 " --> pdb=" O GLY B 755 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY B 755 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 501 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY B 753 " --> pdb=" O LEU B 501 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 497 through 502 removed outlier: 3.908A pdb=" N ALA B 757 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ALA B 499 " --> pdb=" O GLY B 755 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY B 755 " --> pdb=" O ALA B 499 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 501 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY B 753 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N MET B 518 " --> pdb=" O TYR B 754 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 668 through 670 removed outlier: 6.738A pdb=" N ALA B 668 " --> pdb=" O ALA B 723 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU B 725 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLY B 670 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N GLU B 727 " --> pdb=" O GLY B 670 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N PHE B 722 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LYS B 527 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 524 " --> pdb=" O VAL B 745 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 77 through 79 1069 hydrogen bonds defined for protein. 3087 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: 3.46 Time building geometry restraints manager: 2.01 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: 3104 1.33 - 1.45: 5213 1.45 - 1.57: 10681 1.57 - 1.69: 4 1.69 - 1.82: 208 Bond restraints: 19210 Sorted by residual: bond pdb=" C08 E2Q C1004 " pdb=" C09 E2Q C1004 " ideal model delta sigma weight residual 1.422 1.475 -0.053 2.00e-02 2.50e+03 6.91e+00 bond pdb=" C08 E2Q A1003 " pdb=" C09 E2Q A1003 " ideal model delta sigma weight residual 1.422 1.474 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" N CYS D 837 " pdb=" CA CYS D 837 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.26e+00 bond pdb=" N CYS C 837 " pdb=" CA CYS C 837 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 6.00e+00 bond pdb=" N CYS B 837 " pdb=" CA CYS B 837 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 5.95e+00 ... (remaining 19205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 25151 1.42 - 2.84: 577 2.84 - 4.25: 113 4.25 - 5.67: 29 5.67 - 7.09: 6 Bond angle restraints: 25876 Sorted by residual: angle pdb=" CA CYS C 837 " pdb=" C CYS C 837 " pdb=" O CYS C 837 " ideal model delta sigma weight residual 120.82 117.80 3.02 1.05e+00 9.07e-01 8.29e+00 angle pdb=" CA CYS A 837 " pdb=" C CYS A 837 " pdb=" O CYS A 837 " ideal model delta sigma weight residual 120.82 117.87 2.95 1.05e+00 9.07e-01 7.91e+00 angle pdb=" CA CYS D 837 " pdb=" C CYS D 837 " pdb=" O CYS D 837 " ideal model delta sigma weight residual 120.55 117.84 2.71 1.06e+00 8.90e-01 6.54e+00 angle pdb=" CA CYS B 837 " pdb=" C CYS B 837 " pdb=" O CYS B 837 " ideal model delta sigma weight residual 120.55 117.89 2.66 1.06e+00 8.90e-01 6.30e+00 angle pdb=" C MET G 117 " pdb=" N GLY G 118 " pdb=" CA GLY G 118 " ideal model delta sigma weight residual 119.99 122.77 -2.78 1.13e+00 7.83e-01 6.06e+00 ... (remaining 25871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.40: 10744 20.40 - 40.80: 509 40.80 - 61.20: 84 61.20 - 81.60: 16 81.60 - 102.00: 7 Dihedral angle restraints: 11360 sinusoidal: 4574 harmonic: 6786 Sorted by residual: dihedral pdb=" CB CYS C 611 " pdb=" SG CYS C 611 " pdb=" SG CYS B 611 " pdb=" CB CYS B 611 " ideal model delta sinusoidal sigma weight residual -86.00 -20.27 -65.73 1 1.00e+01 1.00e-02 5.65e+01 dihedral pdb=" CB CYS D 611 " pdb=" SG CYS D 611 " pdb=" SG CYS A 611 " pdb=" CB CYS A 611 " ideal model delta sinusoidal sigma weight residual -86.00 -21.75 -64.25 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" C24 OLC A1002 " pdb=" C21 OLC A1002 " pdb=" C22 OLC A1002 " pdb=" O20 OLC A1002 " ideal model delta sinusoidal sigma weight residual 182.78 80.78 102.00 1 3.00e+01 1.11e-03 1.29e+01 ... (remaining 11357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1826 0.030 - 0.059: 666 0.059 - 0.089: 235 0.089 - 0.118: 105 0.118 - 0.148: 20 Chirality restraints: 2852 Sorted by residual: chirality pdb=" CA ILE A 496 " pdb=" N ILE A 496 " pdb=" C ILE A 496 " pdb=" CB ILE A 496 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA ILE C 496 " pdb=" N ILE C 496 " pdb=" C ILE C 496 " pdb=" CB ILE C 496 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE D 481 " pdb=" N ILE D 481 " pdb=" C ILE D 481 " pdb=" CB ILE D 481 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 2849 not shown) Planarity restraints: 3164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLC A1002 " 0.090 2.00e-02 2.50e+03 9.26e-02 8.57e+01 pdb=" C11 OLC A1002 " -0.092 2.00e-02 2.50e+03 pdb=" C8 OLC A1002 " -0.093 2.00e-02 2.50e+03 pdb=" C9 OLC A1002 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC C1003 " 0.075 2.00e-02 2.50e+03 7.29e-02 5.31e+01 pdb=" C11 OLC C1003 " -0.073 2.00e-02 2.50e+03 pdb=" C8 OLC C1003 " -0.072 2.00e-02 2.50e+03 pdb=" C9 OLC C1003 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC B1002 " 0.050 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C11 OLC B1002 " -0.022 2.00e-02 2.50e+03 pdb=" C8 OLC B1002 " 0.022 2.00e-02 2.50e+03 pdb=" C9 OLC B1002 " -0.050 2.00e-02 2.50e+03 ... (remaining 3161 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4172 2.78 - 3.31: 17253 3.31 - 3.84: 30781 3.84 - 4.37: 37575 4.37 - 4.90: 63570 Nonbonded interactions: 153351 Sorted by model distance: nonbonded pdb=" NH1 ARG B 507 " pdb=" O20 E2Q B1003 " model vdw 2.253 3.120 nonbonded pdb=" OE2 GLU C 424 " pdb=" N14 E2Q C1004 " model vdw 2.261 3.120 nonbonded pdb=" NH2 ARG C 507 " pdb=" O22 E2Q C1004 " model vdw 2.263 3.120 nonbonded pdb=" O ILE H 122 " pdb=" OG SER H 125 " model vdw 2.271 3.040 nonbonded pdb=" O ILE F 122 " pdb=" OG SER F 125 " model vdw 2.271 3.040 ... (remaining 153346 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 419 through 595 or resid 597 through 1001)) selection = (chain 'B' and (resid 419 through 595 or resid 597 through 796 or resid 807 thro \ ugh 1001)) selection = (chain 'C' and (resid 419 through 595 or resid 597 through 1001)) selection = (chain 'D' and (resid 419 through 595 or resid 597 through 796 or resid 807 thro \ ugh 1001)) } ncs_group { reference = (chain 'E' and (resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 or resid 56 through 84 or (resid 85 and (na \ me N or name CA or name C or name O or name CB )) or resid 93 through 163 or res \ id 173 through 214)) selection = (chain 'F' and (resid 7 through 71 or (resid 72 through 74 and (name N or name C \ A or name C or name O or name CB )) or resid 75 through 90 or resid 93 through 2 \ 14)) selection = (chain 'G' and (resid 7 through 40 or (resid 41 and (name N or name CA or name C \ or name O or name CB )) or resid 42 or resid 56 through 84 or (resid 85 and (na \ me N or name CA or name C or name O or name CB )) or resid 93 through 163 or res \ id 173 through 214)) selection = (chain 'H' and (resid 7 through 71 or (resid 72 through 74 and (name N or name C \ A or name C or name O or name CB )) or resid 75 through 90 or resid 93 through 2 \ 14)) } 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=0.50 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: 13.500 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.640 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.003 0.053 19228 Z= 0.169 Angle : 0.543 7.088 25904 Z= 0.280 Chirality : 0.039 0.148 2852 Planarity : 0.008 0.101 3164 Dihedral : 12.324 102.002 6982 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: -1.59 (0.17), residues: 2312 helix: -0.03 (0.15), residues: 1308 sheet: -2.88 (0.40), residues: 146 loop : -2.28 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.004 ARG H 131 TYR 0.009 0.001 TYR B 430 PHE 0.011 0.001 PHE C 563 TRP 0.019 0.001 TRP F 33 HIS 0.007 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00338 (19210) covalent geometry : angle 0.54127 (25876) SS BOND : bond 0.00696 ( 14) SS BOND : angle 1.43973 ( 28) hydrogen bonds : bond 0.23200 ( 1067) hydrogen bonds : angle 7.03215 ( 3087) Misc. bond : bond 0.00346 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 ARG cc_start: 0.6757 (mtm-85) cc_final: 0.6507 (mtm-85) REVERT: H 129 LYS cc_start: 0.8013 (mttt) cc_final: 0.7713 (mtpt) REVERT: D 512 ASP cc_start: 0.6637 (m-30) cc_final: 0.6084 (m-30) REVERT: D 660 ASP cc_start: 0.7737 (m-30) cc_final: 0.7421 (m-30) REVERT: A 491 TYR cc_start: 0.7349 (m-10) cc_final: 0.7055 (m-10) REVERT: A 513 PHE cc_start: 0.8551 (m-80) cc_final: 0.8336 (m-80) REVERT: A 525 MET cc_start: 0.7253 (ttp) cc_final: 0.6908 (ttp) REVERT: A 714 ARG cc_start: 0.7010 (ttt180) cc_final: 0.6768 (ttt180) REVERT: A 780 VAL cc_start: 0.8395 (t) cc_final: 0.7922 (t) REVERT: A 781 LEU cc_start: 0.7189 (mt) cc_final: 0.6895 (mp) REVERT: G 99 ARG cc_start: 0.6876 (mtt180) cc_final: 0.6377 (mmm160) REVERT: G 131 ARG cc_start: 0.7298 (mtt180) cc_final: 0.6313 (mmm160) REVERT: E 65 ARG cc_start: 0.7026 (mtm-85) cc_final: 0.6377 (mtm180) REVERT: E 99 ARG cc_start: 0.6827 (mtt180) cc_final: 0.6389 (mmm160) REVERT: E 131 ARG cc_start: 0.7396 (mtt180) cc_final: 0.6325 (mmm160) REVERT: E 192 MET cc_start: 0.8223 (mtm) cc_final: 0.8021 (mtp) REVERT: C 442 LYS cc_start: 0.6745 (mtmt) cc_final: 0.6522 (tttm) REVERT: C 463 LYS cc_start: 0.7380 (tttt) cc_final: 0.6711 (pmtt) REVERT: C 525 MET cc_start: 0.6923 (ttp) cc_final: 0.6627 (ttp) REVERT: C 714 ARG cc_start: 0.6953 (ttt180) cc_final: 0.6724 (ttt180) REVERT: C 780 VAL cc_start: 0.8588 (t) cc_final: 0.8310 (t) REVERT: B 512 ASP cc_start: 0.6064 (m-30) cc_final: 0.4700 (p0) REVERT: B 660 ASP cc_start: 0.8154 (m-30) cc_final: 0.7884 (m-30) REVERT: B 788 TRP cc_start: 0.7056 (m100) cc_final: 0.6791 (m100) REVERT: F 11 LEU cc_start: 0.8465 (tp) cc_final: 0.8246 (tp) REVERT: F 65 ARG cc_start: 0.6793 (mtm-85) cc_final: 0.6511 (mtm-85) REVERT: F 129 LYS cc_start: 0.8125 (mttt) cc_final: 0.7752 (mtpt) outliers start: 0 outliers final: 1 residues processed: 428 average time/residue: 0.6504 time to fit residues: 308.2106 Evaluate side-chains 266 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 14 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 107 optimal weight: 0.0040 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 149 ASN H 199 HIS D 433 ASN D 457 HIS A 813 ASN G 9 GLN E 9 GLN B 433 ASN B 457 HIS F 149 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.204568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127162 restraints weight = 27107.585| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.90 r_work: 0.3191 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3012 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19228 Z= 0.147 Angle : 0.577 8.485 25904 Z= 0.298 Chirality : 0.041 0.169 2852 Planarity : 0.004 0.041 3164 Dihedral : 8.425 74.547 2908 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.31 % Rotamer: Outliers : 1.82 % Allowed : 11.19 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: 0.23 (0.18), residues: 2312 helix: 1.45 (0.15), residues: 1332 sheet: -2.37 (0.47), residues: 120 loop : -1.57 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 507 TYR 0.011 0.001 TYR F 181 PHE 0.015 0.002 PHE A 537 TRP 0.027 0.001 TRP A 788 HIS 0.006 0.002 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00331 (19210) covalent geometry : angle 0.57669 (25876) SS BOND : bond 0.00332 ( 14) SS BOND : angle 0.91631 ( 28) hydrogen bonds : bond 0.04860 ( 1067) hydrogen bonds : angle 4.06655 ( 3087) Misc. bond : bond 0.00040 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 301 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 65 ARG cc_start: 0.7079 (mtm-85) cc_final: 0.6832 (mtm-85) REVERT: H 99 ARG cc_start: 0.7491 (mtm180) cc_final: 0.6538 (mmm160) REVERT: H 126 GLU cc_start: 0.7427 (mm-30) cc_final: 0.7197 (mm-30) REVERT: H 129 LYS cc_start: 0.7987 (mttt) cc_final: 0.7663 (mtpt) REVERT: D 660 ASP cc_start: 0.7608 (m-30) cc_final: 0.7323 (m-30) REVERT: D 748 ASN cc_start: 0.8283 (m-40) cc_final: 0.7955 (m-40) REVERT: A 442 LYS cc_start: 0.7143 (mtmt) cc_final: 0.6432 (mmpt) REVERT: A 491 TYR cc_start: 0.7394 (m-10) cc_final: 0.6884 (m-10) REVERT: A 656 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7037 (tp30) REVERT: G 10 MET cc_start: 0.8330 (tpp) cc_final: 0.7951 (tpt) REVERT: G 65 ARG cc_start: 0.7141 (mtm-85) cc_final: 0.6917 (mtm-85) REVERT: G 99 ARG cc_start: 0.7134 (mtt180) cc_final: 0.6282 (mmm160) REVERT: G 131 ARG cc_start: 0.7514 (mtt180) cc_final: 0.6227 (mmm160) REVERT: E 99 ARG cc_start: 0.7167 (mtt180) cc_final: 0.6322 (mmm160) REVERT: E 131 ARG cc_start: 0.7577 (mtt180) cc_final: 0.6267 (mmm160) REVERT: C 463 LYS cc_start: 0.7355 (tttt) cc_final: 0.6677 (pmtt) REVERT: C 685 LYS cc_start: 0.8409 (mmmt) cc_final: 0.8105 (mmpt) REVERT: C 733 TYR cc_start: 0.5665 (t80) cc_final: 0.5424 (t80) REVERT: B 436 MET cc_start: 0.5685 (mpp) cc_final: 0.4673 (mpt) REVERT: B 463 LYS cc_start: 0.8358 (tttt) cc_final: 0.7992 (ttpt) REVERT: B 523 SER cc_start: 0.8685 (m) cc_final: 0.8209 (p) REVERT: B 660 ASP cc_start: 0.7964 (m-30) cc_final: 0.7707 (m-30) REVERT: B 705 THR cc_start: 0.8005 (p) cc_final: 0.7634 (t) REVERT: F 65 ARG cc_start: 0.7075 (mtm-85) cc_final: 0.6823 (mtm-85) REVERT: F 99 ARG cc_start: 0.7417 (mtm180) cc_final: 0.6566 (mmm160) REVERT: F 126 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7174 (mm-30) REVERT: F 129 LYS cc_start: 0.8138 (mttt) cc_final: 0.7808 (mtpt) REVERT: F 204 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.6974 (mmm160) outliers start: 35 outliers final: 15 residues processed: 323 average time/residue: 0.7211 time to fit residues: 258.0090 Evaluate side-chains 264 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 249 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 429 MET Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain F residue 14 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 223 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 110 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 69 optimal weight: 0.0370 chunk 9 optimal weight: 0.6980 chunk 216 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS D 457 HIS ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.205582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129338 restraints weight = 32420.248| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.22 r_work: 0.3180 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3055 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19228 Z= 0.116 Angle : 0.522 7.576 25904 Z= 0.269 Chirality : 0.040 0.202 2852 Planarity : 0.004 0.037 3164 Dihedral : 8.155 75.019 2908 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.34 % Favored : 97.53 % Rotamer: Outliers : 2.03 % Allowed : 13.84 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: 0.92 (0.18), residues: 2312 helix: 2.06 (0.14), residues: 1332 sheet: -2.42 (0.40), residues: 156 loop : -1.22 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 706 TYR 0.022 0.001 TYR C 446 PHE 0.014 0.001 PHE C 606 TRP 0.017 0.001 TRP A 788 HIS 0.006 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00254 (19210) covalent geometry : angle 0.52231 (25876) SS BOND : bond 0.00224 ( 14) SS BOND : angle 0.54528 ( 28) hydrogen bonds : bond 0.04210 ( 1067) hydrogen bonds : angle 3.78906 ( 3087) Misc. bond : bond 0.00009 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 275 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.7934 (mtt-85) cc_final: 0.7604 (mtt-85) REVERT: H 65 ARG cc_start: 0.6678 (mtm-85) cc_final: 0.6438 (mtm-85) REVERT: H 99 ARG cc_start: 0.7014 (mtm180) cc_final: 0.6009 (mmm160) REVERT: H 129 LYS cc_start: 0.7840 (mttt) cc_final: 0.7500 (mtpt) REVERT: D 436 MET cc_start: 0.5801 (mpp) cc_final: 0.5000 (mtm) REVERT: D 660 ASP cc_start: 0.7211 (m-30) cc_final: 0.6935 (m-30) REVERT: D 748 ASN cc_start: 0.8148 (m-40) cc_final: 0.7758 (m-40) REVERT: A 442 LYS cc_start: 0.7101 (mtmt) cc_final: 0.6455 (mmpt) REVERT: A 491 TYR cc_start: 0.7457 (m-10) cc_final: 0.6889 (m-10) REVERT: A 656 GLU cc_start: 0.7405 (mt-10) cc_final: 0.6606 (tp30) REVERT: G 10 MET cc_start: 0.7974 (tpp) cc_final: 0.7684 (tpt) REVERT: G 65 ARG cc_start: 0.6893 (mtm-85) cc_final: 0.6634 (mtm-85) REVERT: G 99 ARG cc_start: 0.6655 (mtt180) cc_final: 0.5797 (mmm160) REVERT: G 131 ARG cc_start: 0.7319 (mtt180) cc_final: 0.6002 (mmm160) REVERT: G 204 ARG cc_start: 0.6642 (tpp80) cc_final: 0.6367 (mpt180) REVERT: E 11 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7436 (tm) REVERT: E 99 ARG cc_start: 0.6742 (mtt180) cc_final: 0.5892 (mmm160) REVERT: E 131 ARG cc_start: 0.7385 (mtt180) cc_final: 0.6013 (mmm160) REVERT: C 463 LYS cc_start: 0.7432 (tttt) cc_final: 0.6629 (pmtt) REVERT: C 685 LYS cc_start: 0.8290 (mmmt) cc_final: 0.8015 (mmpt) REVERT: C 733 TYR cc_start: 0.5363 (t80) cc_final: 0.5131 (t80) REVERT: C 777 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: B 436 MET cc_start: 0.5696 (mpp) cc_final: 0.5258 (mtm) REVERT: B 463 LYS cc_start: 0.8250 (tttt) cc_final: 0.7830 (ttpt) REVERT: B 523 SER cc_start: 0.8462 (OUTLIER) cc_final: 0.7957 (p) REVERT: B 660 ASP cc_start: 0.7513 (m-30) cc_final: 0.7306 (m-30) REVERT: B 683 ARG cc_start: 0.7229 (mtm180) cc_final: 0.6928 (ptt-90) REVERT: B 705 THR cc_start: 0.7760 (p) cc_final: 0.7444 (t) REVERT: B 719 LYS cc_start: 0.7249 (mmtt) cc_final: 0.7027 (mttm) REVERT: F 65 ARG cc_start: 0.6701 (mtm-85) cc_final: 0.6449 (mtm-85) REVERT: F 99 ARG cc_start: 0.6947 (mtm180) cc_final: 0.6046 (mmm160) REVERT: F 129 LYS cc_start: 0.8000 (mttt) cc_final: 0.7632 (mtpt) REVERT: F 204 ARG cc_start: 0.7500 (mmt-90) cc_final: 0.6637 (mmm160) outliers start: 39 outliers final: 11 residues processed: 293 average time/residue: 0.6647 time to fit residues: 216.8852 Evaluate side-chains 250 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 236 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain F residue 22 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 230 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 22 optimal weight: 0.0170 chunk 229 optimal weight: 3.9990 chunk 167 optimal weight: 0.3980 chunk 134 optimal weight: 3.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS D 608 GLN A 664 GLN ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 GLN ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.205370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.130146 restraints weight = 25210.738| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.89 r_work: 0.3205 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19228 Z= 0.114 Angle : 0.505 7.191 25904 Z= 0.258 Chirality : 0.040 0.266 2852 Planarity : 0.004 0.035 3164 Dihedral : 8.051 73.036 2906 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.17 % Favored : 97.70 % Rotamer: Outliers : 2.08 % Allowed : 14.78 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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 (0.18), residues: 2312 helix: 2.27 (0.14), residues: 1336 sheet: -2.22 (0.40), residues: 156 loop : -1.00 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 616 TYR 0.019 0.001 TYR C 446 PHE 0.014 0.001 PHE C 606 TRP 0.013 0.001 TRP A 788 HIS 0.005 0.001 HIS F 60 Details of bonding type rmsd covalent geometry : bond 0.00252 (19210) covalent geometry : angle 0.50464 (25876) SS BOND : bond 0.00176 ( 14) SS BOND : angle 0.38952 ( 28) hydrogen bonds : bond 0.04003 ( 1067) hydrogen bonds : angle 3.70076 ( 3087) Misc. bond : bond 0.00004 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 37 ARG cc_start: 0.7986 (mtt-85) cc_final: 0.7641 (mtt-85) REVERT: H 99 ARG cc_start: 0.7110 (mtm180) cc_final: 0.6078 (mmm160) REVERT: H 129 LYS cc_start: 0.7886 (mttt) cc_final: 0.7533 (mtpt) REVERT: D 436 MET cc_start: 0.5888 (mpp) cc_final: 0.5379 (mtm) REVERT: D 660 ASP cc_start: 0.7231 (m-30) cc_final: 0.6994 (m-30) REVERT: D 748 ASN cc_start: 0.8203 (m-40) cc_final: 0.7841 (m-40) REVERT: A 491 TYR cc_start: 0.7435 (m-10) cc_final: 0.6857 (m-10) REVERT: A 656 GLU cc_start: 0.7460 (mt-10) cc_final: 0.6657 (tp30) REVERT: G 10 MET cc_start: 0.8105 (tpp) cc_final: 0.7864 (tpt) REVERT: G 99 ARG cc_start: 0.6754 (mtt180) cc_final: 0.5902 (mmm160) REVERT: G 131 ARG cc_start: 0.7361 (mtt180) cc_final: 0.6043 (mmm160) REVERT: G 204 ARG cc_start: 0.6798 (tpp80) cc_final: 0.6453 (mpt180) REVERT: E 99 ARG cc_start: 0.6856 (mtt180) cc_final: 0.5979 (mmm160) REVERT: E 131 ARG cc_start: 0.7484 (mtt180) cc_final: 0.6155 (mmm160) REVERT: E 204 ARG cc_start: 0.6829 (tpp80) cc_final: 0.6477 (mpt180) REVERT: C 463 LYS cc_start: 0.7347 (tttt) cc_final: 0.6543 (pmtt) REVERT: C 733 TYR cc_start: 0.5415 (t80) cc_final: 0.5157 (t80) REVERT: C 777 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6677 (mp0) REVERT: C 829 MET cc_start: 0.8922 (mtm) cc_final: 0.8714 (mtp) REVERT: B 436 MET cc_start: 0.5803 (mpp) cc_final: 0.5468 (mtm) REVERT: B 463 LYS cc_start: 0.8275 (tttt) cc_final: 0.7889 (ttpt) REVERT: B 523 SER cc_start: 0.8477 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 660 ASP cc_start: 0.7486 (m-30) cc_final: 0.7202 (m-30) REVERT: B 683 ARG cc_start: 0.7242 (mtm180) cc_final: 0.7033 (ptt-90) REVERT: B 705 THR cc_start: 0.7832 (OUTLIER) cc_final: 0.7518 (t) REVERT: F 65 ARG cc_start: 0.6697 (mtm-85) cc_final: 0.6492 (mtm-85) REVERT: F 99 ARG cc_start: 0.7049 (mtm180) cc_final: 0.6084 (mmm160) REVERT: F 129 LYS cc_start: 0.8012 (mttt) cc_final: 0.7643 (mtpt) REVERT: F 204 ARG cc_start: 0.7535 (mmt-90) cc_final: 0.6725 (mmm160) outliers start: 40 outliers final: 16 residues processed: 283 average time/residue: 0.6479 time to fit residues: 203.9658 Evaluate side-chains 260 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 780 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 208 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 73 optimal weight: 0.1980 chunk 145 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 232 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS ** D 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.202562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.125803 restraints weight = 24836.061| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 3.12 r_work: 0.3148 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19228 Z= 0.156 Angle : 0.547 8.699 25904 Z= 0.280 Chirality : 0.042 0.291 2852 Planarity : 0.004 0.042 3164 Dihedral : 8.604 75.051 2906 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.56 % Favored : 97.36 % Rotamer: Outliers : 2.29 % Allowed : 15.35 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: 1.17 (0.18), residues: 2312 helix: 2.14 (0.14), residues: 1336 sheet: -2.05 (0.41), residues: 156 loop : -0.98 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 616 TYR 0.019 0.001 TYR C 446 PHE 0.015 0.002 PHE A 537 TRP 0.011 0.001 TRP A 788 HIS 0.006 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00362 (19210) covalent geometry : angle 0.54742 (25876) SS BOND : bond 0.00254 ( 14) SS BOND : angle 0.49935 ( 28) hydrogen bonds : bond 0.04498 ( 1067) hydrogen bonds : angle 3.82525 ( 3087) Misc. bond : bond 0.00015 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 129 LYS cc_start: 0.7979 (mttt) cc_final: 0.7613 (mtpt) REVERT: D 432 LYS cc_start: 0.6272 (pmtt) cc_final: 0.5758 (ttmp) REVERT: D 436 MET cc_start: 0.5982 (mpp) cc_final: 0.5177 (mtm) REVERT: D 660 ASP cc_start: 0.7581 (m-30) cc_final: 0.7376 (m-30) REVERT: D 748 ASN cc_start: 0.8326 (m-40) cc_final: 0.7980 (m-40) REVERT: A 480 LYS cc_start: 0.7039 (mmpt) cc_final: 0.6448 (mmmm) REVERT: A 491 TYR cc_start: 0.7391 (m-10) cc_final: 0.6869 (m-10) REVERT: A 656 GLU cc_start: 0.7476 (mt-10) cc_final: 0.6760 (tp30) REVERT: A 745 VAL cc_start: 0.7546 (OUTLIER) cc_final: 0.7282 (p) REVERT: G 10 MET cc_start: 0.8391 (tpp) cc_final: 0.8146 (tpt) REVERT: G 99 ARG cc_start: 0.7085 (mtt180) cc_final: 0.6224 (mmm160) REVERT: G 131 ARG cc_start: 0.7517 (mtt180) cc_final: 0.6159 (mmm160) REVERT: G 204 ARG cc_start: 0.7230 (tpp80) cc_final: 0.6772 (mpt180) REVERT: E 65 ARG cc_start: 0.7433 (mtp180) cc_final: 0.7065 (mtm-85) REVERT: E 99 ARG cc_start: 0.7102 (mtt180) cc_final: 0.6270 (mmm160) REVERT: E 131 ARG cc_start: 0.7648 (mtt180) cc_final: 0.6299 (mmm160) REVERT: E 147 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8051 (mp) REVERT: E 204 ARG cc_start: 0.7237 (tpp80) cc_final: 0.6791 (mpt180) REVERT: C 463 LYS cc_start: 0.7285 (tttt) cc_final: 0.6584 (pmtt) REVERT: C 685 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7911 (mppt) REVERT: C 777 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: B 436 MET cc_start: 0.5665 (mpp) cc_final: 0.5212 (mtm) REVERT: B 463 LYS cc_start: 0.8340 (tttt) cc_final: 0.7981 (ttpt) REVERT: B 523 SER cc_start: 0.8737 (OUTLIER) cc_final: 0.8395 (p) REVERT: B 660 ASP cc_start: 0.7731 (m-30) cc_final: 0.7441 (m-30) REVERT: B 683 ARG cc_start: 0.7328 (mtm180) cc_final: 0.7065 (ptt-90) REVERT: B 705 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7519 (t) REVERT: F 129 LYS cc_start: 0.8106 (mttt) cc_final: 0.7752 (mtpt) REVERT: F 204 ARG cc_start: 0.7874 (mmt-90) cc_final: 0.7064 (mmm160) outliers start: 44 outliers final: 24 residues processed: 283 average time/residue: 0.7217 time to fit residues: 226.1979 Evaluate side-chains 270 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 241 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain D residue 612 ASP Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 780 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 673 ASP Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 147 LEU Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 22 SER Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 208 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 31 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 70 optimal weight: 0.0370 chunk 220 optimal weight: 2.9990 chunk 154 optimal weight: 0.2980 chunk 83 optimal weight: 0.0070 chunk 14 optimal weight: 0.7980 chunk 197 optimal weight: 0.6980 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS D 608 GLN ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.205228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126423 restraints weight = 30984.923| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 3.04 r_work: 0.3217 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 19228 Z= 0.098 Angle : 0.491 9.752 25904 Z= 0.248 Chirality : 0.040 0.331 2852 Planarity : 0.003 0.041 3164 Dihedral : 7.944 71.824 2906 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.99 % Favored : 97.92 % Rotamer: Outliers : 1.66 % Allowed : 16.65 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: 1.49 (0.18), residues: 2312 helix: 2.42 (0.14), residues: 1340 sheet: -2.10 (0.40), residues: 168 loop : -0.82 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 616 TYR 0.023 0.001 TYR C 733 PHE 0.013 0.001 PHE C 606 TRP 0.009 0.001 TRP C 788 HIS 0.005 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00211 (19210) covalent geometry : angle 0.49104 (25876) SS BOND : bond 0.00135 ( 14) SS BOND : angle 0.25487 ( 28) hydrogen bonds : bond 0.03664 ( 1067) hydrogen bonds : angle 3.60807 ( 3087) Misc. bond : bond 0.00008 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 99 ARG cc_start: 0.7283 (mtm180) cc_final: 0.6191 (mmm160) REVERT: H 129 LYS cc_start: 0.7873 (mttt) cc_final: 0.7450 (mtpt) REVERT: H 204 ARG cc_start: 0.7625 (mmt-90) cc_final: 0.6936 (mtt180) REVERT: D 432 LYS cc_start: 0.6364 (pmtt) cc_final: 0.5875 (ttmp) REVERT: D 436 MET cc_start: 0.6070 (mpp) cc_final: 0.5521 (mtm) REVERT: D 443 TYR cc_start: 0.7254 (m-80) cc_final: 0.6781 (m-80) REVERT: D 660 ASP cc_start: 0.7218 (m-30) cc_final: 0.7010 (m-30) REVERT: D 685 LYS cc_start: 0.7113 (mtmt) cc_final: 0.6387 (tptp) REVERT: D 748 ASN cc_start: 0.8214 (m-40) cc_final: 0.7830 (m-40) REVERT: A 480 LYS cc_start: 0.7049 (mmpt) cc_final: 0.6454 (mmmm) REVERT: A 491 TYR cc_start: 0.7386 (m-10) cc_final: 0.6865 (m-10) REVERT: A 656 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6793 (tp30) REVERT: G 10 MET cc_start: 0.8110 (tpp) cc_final: 0.7854 (tpt) REVERT: G 99 ARG cc_start: 0.6897 (mtt180) cc_final: 0.6033 (mmm160) REVERT: G 131 ARG cc_start: 0.7430 (mtt180) cc_final: 0.6021 (mmm160) REVERT: G 204 ARG cc_start: 0.6970 (tpp80) cc_final: 0.6644 (mpt180) REVERT: E 99 ARG cc_start: 0.6849 (mtt180) cc_final: 0.6001 (mmm160) REVERT: E 131 ARG cc_start: 0.7504 (mtt180) cc_final: 0.6152 (mmm160) REVERT: E 204 ARG cc_start: 0.6957 (tpp80) cc_final: 0.6712 (mpt180) REVERT: C 463 LYS cc_start: 0.7371 (tttt) cc_final: 0.6605 (pmtt) REVERT: C 480 LYS cc_start: 0.7236 (mmpt) cc_final: 0.6686 (mmmt) REVERT: C 685 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7851 (mppt) REVERT: C 733 TYR cc_start: 0.5327 (t80) cc_final: 0.5050 (t80) REVERT: C 777 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: C 829 MET cc_start: 0.8946 (mtm) cc_final: 0.8743 (mtp) REVERT: B 436 MET cc_start: 0.5697 (mpp) cc_final: 0.4924 (mpt) REVERT: B 443 TYR cc_start: 0.7124 (m-80) cc_final: 0.6728 (m-80) REVERT: B 463 LYS cc_start: 0.8285 (tttt) cc_final: 0.7946 (ttpt) REVERT: B 523 SER cc_start: 0.8453 (OUTLIER) cc_final: 0.8231 (p) REVERT: B 660 ASP cc_start: 0.7403 (m-30) cc_final: 0.7116 (m-30) REVERT: B 705 THR cc_start: 0.7677 (p) cc_final: 0.7385 (t) REVERT: B 719 LYS cc_start: 0.7053 (mmtt) cc_final: 0.6763 (mttm) REVERT: F 99 ARG cc_start: 0.7268 (mtm180) cc_final: 0.6184 (mmm160) REVERT: F 129 LYS cc_start: 0.7978 (mttt) cc_final: 0.7586 (mtpt) REVERT: F 204 ARG cc_start: 0.7614 (mmt-90) cc_final: 0.6845 (mmm160) outliers start: 32 outliers final: 17 residues processed: 270 average time/residue: 0.6871 time to fit residues: 205.5841 Evaluate side-chains 257 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain D residue 612 ASP Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 523 SER Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 208 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 57 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 201 optimal weight: 0.9980 chunk 227 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 19 optimal weight: 0.0070 chunk 75 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 731 ASN B 608 GLN ** B 664 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 = 0.4300 r_free = 0.4300 target = 0.204554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.124076 restraints weight = 33700.317| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.64 r_work: 0.3206 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19228 Z= 0.107 Angle : 0.500 9.183 25904 Z= 0.252 Chirality : 0.040 0.311 2852 Planarity : 0.003 0.038 3164 Dihedral : 7.850 68.676 2906 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.95 % Favored : 97.96 % Rotamer: Outliers : 1.56 % Allowed : 16.96 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: 1.57 (0.18), residues: 2312 helix: 2.46 (0.14), residues: 1340 sheet: -2.02 (0.39), residues: 168 loop : -0.74 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 616 TYR 0.020 0.001 TYR C 733 PHE 0.013 0.001 PHE C 606 TRP 0.009 0.001 TRP A 788 HIS 0.005 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00235 (19210) covalent geometry : angle 0.49992 (25876) SS BOND : bond 0.00148 ( 14) SS BOND : angle 0.30078 ( 28) hydrogen bonds : bond 0.03783 ( 1067) hydrogen bonds : angle 3.60860 ( 3087) Misc. bond : bond 0.00003 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 99 ARG cc_start: 0.7540 (mtm180) cc_final: 0.6406 (mmm160) REVERT: H 129 LYS cc_start: 0.7928 (mttt) cc_final: 0.7508 (mtpt) REVERT: H 204 ARG cc_start: 0.7777 (mmt-90) cc_final: 0.7055 (mmm160) REVERT: D 429 MET cc_start: 0.5216 (mtp) cc_final: 0.4749 (mtm) REVERT: D 432 LYS cc_start: 0.6347 (pmtt) cc_final: 0.5821 (ttmp) REVERT: D 436 MET cc_start: 0.6068 (mpp) cc_final: 0.5000 (mpt) REVERT: D 443 TYR cc_start: 0.7314 (m-80) cc_final: 0.6873 (m-80) REVERT: D 656 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7745 (mt-10) REVERT: D 660 ASP cc_start: 0.7253 (m-30) cc_final: 0.7024 (m-30) REVERT: D 748 ASN cc_start: 0.8279 (m-40) cc_final: 0.7915 (m-40) REVERT: A 480 LYS cc_start: 0.7022 (mmpt) cc_final: 0.6407 (mmmm) REVERT: A 491 TYR cc_start: 0.7405 (m-10) cc_final: 0.6878 (m-10) REVERT: A 656 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7069 (mm-30) REVERT: G 10 MET cc_start: 0.8260 (tpp) cc_final: 0.8030 (tpt) REVERT: G 99 ARG cc_start: 0.7069 (mtt180) cc_final: 0.6214 (mmm160) REVERT: G 131 ARG cc_start: 0.7556 (mtt180) cc_final: 0.6199 (mmm160) REVERT: G 204 ARG cc_start: 0.7138 (tpp80) cc_final: 0.6774 (mpt180) REVERT: E 99 ARG cc_start: 0.7074 (mtt180) cc_final: 0.6240 (mmm160) REVERT: E 131 ARG cc_start: 0.7595 (mtt180) cc_final: 0.6270 (mmm160) REVERT: E 204 ARG cc_start: 0.7092 (tpp80) cc_final: 0.6792 (mpt180) REVERT: C 463 LYS cc_start: 0.7352 (tttt) cc_final: 0.6582 (pmtt) REVERT: C 480 LYS cc_start: 0.7260 (mmpt) cc_final: 0.6656 (mmmt) REVERT: C 733 TYR cc_start: 0.5465 (t80) cc_final: 0.5186 (t80) REVERT: B 422 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7181 (mm) REVERT: B 429 MET cc_start: 0.4954 (mtp) cc_final: 0.4584 (mtm) REVERT: B 436 MET cc_start: 0.5684 (mpp) cc_final: 0.4940 (mpt) REVERT: B 443 TYR cc_start: 0.7164 (m-80) cc_final: 0.6744 (m-80) REVERT: B 463 LYS cc_start: 0.8310 (tttt) cc_final: 0.7987 (ttpt) REVERT: B 660 ASP cc_start: 0.7501 (m-30) cc_final: 0.7256 (m-30) REVERT: B 705 THR cc_start: 0.7716 (p) cc_final: 0.7363 (t) REVERT: B 719 LYS cc_start: 0.7052 (mmtt) cc_final: 0.6776 (mttm) REVERT: F 99 ARG cc_start: 0.7485 (mtm180) cc_final: 0.6394 (mmm160) REVERT: F 129 LYS cc_start: 0.8067 (mttt) cc_final: 0.7700 (mtpt) REVERT: F 204 ARG cc_start: 0.7764 (mmt-90) cc_final: 0.7055 (mmm160) outliers start: 30 outliers final: 17 residues processed: 271 average time/residue: 0.7571 time to fit residues: 226.7637 Evaluate side-chains 261 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain D residue 612 ASP Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 780 VAL Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 89 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 211 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 216 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.202203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.122608 restraints weight = 28946.408| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.72 r_work: 0.3165 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19228 Z= 0.145 Angle : 0.538 8.450 25904 Z= 0.272 Chirality : 0.041 0.306 2852 Planarity : 0.004 0.059 3164 Dihedral : 8.319 70.721 2906 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.17 % Favored : 97.75 % Rotamer: Outliers : 1.82 % Allowed : 17.27 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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 (0.18), residues: 2312 helix: 2.32 (0.14), residues: 1338 sheet: -1.98 (0.39), residues: 170 loop : -0.71 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 706 TYR 0.021 0.001 TYR C 446 PHE 0.014 0.001 PHE C 606 TRP 0.010 0.001 TRP C 788 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00339 (19210) covalent geometry : angle 0.53828 (25876) SS BOND : bond 0.00207 ( 14) SS BOND : angle 0.48438 ( 28) hydrogen bonds : bond 0.04285 ( 1067) hydrogen bonds : angle 3.73580 ( 3087) Misc. bond : bond 0.00021 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 99 ARG cc_start: 0.7599 (mtm180) cc_final: 0.6514 (mmm160) REVERT: H 129 LYS cc_start: 0.8006 (mttt) cc_final: 0.7644 (mtpt) REVERT: D 423 MET cc_start: 0.6879 (OUTLIER) cc_final: 0.6229 (tmt) REVERT: D 429 MET cc_start: 0.5462 (mtp) cc_final: 0.5105 (mtm) REVERT: D 432 LYS cc_start: 0.6414 (pmtt) cc_final: 0.5887 (ttmp) REVERT: D 436 MET cc_start: 0.6111 (mpp) cc_final: 0.5078 (mpt) REVERT: D 443 TYR cc_start: 0.7196 (m-80) cc_final: 0.6941 (m-80) REVERT: D 656 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7819 (mt-10) REVERT: D 660 ASP cc_start: 0.7407 (m-30) cc_final: 0.7148 (m-30) REVERT: D 678 LYS cc_start: 0.7340 (tttt) cc_final: 0.7071 (tttt) REVERT: D 685 LYS cc_start: 0.7135 (mtmt) cc_final: 0.6891 (pptt) REVERT: D 690 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6729 (mm-30) REVERT: D 748 ASN cc_start: 0.8330 (m-40) cc_final: 0.7976 (m-40) REVERT: A 480 LYS cc_start: 0.7038 (mmpt) cc_final: 0.6412 (mmmm) REVERT: A 491 TYR cc_start: 0.7330 (m-10) cc_final: 0.6828 (m-10) REVERT: A 656 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7063 (mm-30) REVERT: A 841 ARG cc_start: 0.7130 (ttp80) cc_final: 0.6889 (ptt90) REVERT: G 10 MET cc_start: 0.8359 (tpp) cc_final: 0.8115 (tpt) REVERT: G 99 ARG cc_start: 0.7094 (mtt180) cc_final: 0.6263 (mmm160) REVERT: G 131 ARG cc_start: 0.7602 (mtt180) cc_final: 0.6228 (mmm160) REVERT: G 204 ARG cc_start: 0.7190 (tpp80) cc_final: 0.6758 (mpt180) REVERT: E 99 ARG cc_start: 0.7132 (mtt180) cc_final: 0.6316 (mmm160) REVERT: E 131 ARG cc_start: 0.7671 (mtt180) cc_final: 0.6368 (mmm160) REVERT: E 204 ARG cc_start: 0.7205 (tpp80) cc_final: 0.6797 (mpt180) REVERT: C 463 LYS cc_start: 0.7328 (tttt) cc_final: 0.6630 (pmtt) REVERT: C 685 LYS cc_start: 0.8350 (mmmt) cc_final: 0.7291 (pttt) REVERT: C 733 TYR cc_start: 0.5497 (t80) cc_final: 0.5251 (t80) REVERT: B 422 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.6999 (mm) REVERT: B 423 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6526 (tmt) REVERT: B 429 MET cc_start: 0.5155 (mtp) cc_final: 0.4650 (mtm) REVERT: B 436 MET cc_start: 0.5741 (mpp) cc_final: 0.4996 (mpt) REVERT: B 443 TYR cc_start: 0.7178 (m-80) cc_final: 0.6879 (m-80) REVERT: B 463 LYS cc_start: 0.8359 (tttt) cc_final: 0.8031 (ttpt) REVERT: B 485 MET cc_start: 0.7424 (mtp) cc_final: 0.6765 (mtm) REVERT: B 660 ASP cc_start: 0.7609 (m-30) cc_final: 0.7329 (m-30) REVERT: B 719 LYS cc_start: 0.7122 (mmtt) cc_final: 0.6855 (mttm) REVERT: F 129 LYS cc_start: 0.8112 (mttt) cc_final: 0.7764 (mtpt) REVERT: F 204 ARG cc_start: 0.7832 (mmt-90) cc_final: 0.7079 (mmm160) outliers start: 35 outliers final: 19 residues processed: 272 average time/residue: 0.7662 time to fit residues: 230.2606 Evaluate side-chains 266 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 612 ASP Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 780 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain C residue 612 ASP Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 221 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 222 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.201574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.123231 restraints weight = 28161.010| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 3.24 r_work: 0.3120 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19228 Z= 0.158 Angle : 0.553 9.935 25904 Z= 0.280 Chirality : 0.042 0.350 2852 Planarity : 0.004 0.054 3164 Dihedral : 8.619 73.819 2906 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.87 % Allowed : 17.59 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: 1.37 (0.18), residues: 2312 helix: 2.22 (0.14), residues: 1338 sheet: -1.86 (0.39), residues: 170 loop : -0.72 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 706 TYR 0.020 0.002 TYR A 446 PHE 0.015 0.001 PHE A 606 TRP 0.012 0.001 TRP A 788 HIS 0.006 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00370 (19210) covalent geometry : angle 0.55335 (25876) SS BOND : bond 0.00224 ( 14) SS BOND : angle 0.53312 ( 28) hydrogen bonds : bond 0.04395 ( 1067) hydrogen bonds : angle 3.79575 ( 3087) Misc. bond : bond 0.00027 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 259 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: H 129 LYS cc_start: 0.7980 (mttt) cc_final: 0.7606 (mtpt) REVERT: D 423 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6135 (tmt) REVERT: D 429 MET cc_start: 0.5338 (mtp) cc_final: 0.4984 (mtm) REVERT: D 432 LYS cc_start: 0.6461 (pmtt) cc_final: 0.5912 (ttmp) REVERT: D 436 MET cc_start: 0.6378 (mpp) cc_final: 0.5146 (mpt) REVERT: D 656 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7874 (mt-10) REVERT: D 678 LYS cc_start: 0.7350 (tttt) cc_final: 0.6999 (ttpp) REVERT: D 685 LYS cc_start: 0.7147 (mtmt) cc_final: 0.6683 (pptt) REVERT: D 748 ASN cc_start: 0.8308 (m-40) cc_final: 0.7961 (m-40) REVERT: A 480 LYS cc_start: 0.7158 (mmpt) cc_final: 0.6558 (mmmm) REVERT: A 491 TYR cc_start: 0.7320 (m-10) cc_final: 0.6774 (m-10) REVERT: A 656 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7008 (mm-30) REVERT: G 99 ARG cc_start: 0.7110 (mtt180) cc_final: 0.6265 (mmm160) REVERT: G 131 ARG cc_start: 0.7581 (mtt180) cc_final: 0.6212 (mmm160) REVERT: G 204 ARG cc_start: 0.7191 (tpp80) cc_final: 0.6745 (mpt180) REVERT: E 99 ARG cc_start: 0.7104 (mtt180) cc_final: 0.6281 (mmm160) REVERT: E 131 ARG cc_start: 0.7626 (mtt180) cc_final: 0.6308 (mmm160) REVERT: E 204 ARG cc_start: 0.7160 (tpp80) cc_final: 0.6755 (mpt180) REVERT: C 463 LYS cc_start: 0.7425 (tttt) cc_final: 0.6659 (pmtt) REVERT: C 671 THR cc_start: 0.6846 (p) cc_final: 0.6546 (p) REVERT: C 685 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7266 (pttt) REVERT: B 422 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7191 (mm) REVERT: B 423 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6426 (tmt) REVERT: B 429 MET cc_start: 0.5218 (mtp) cc_final: 0.4738 (mtm) REVERT: B 436 MET cc_start: 0.5958 (mpp) cc_final: 0.5258 (mpt) REVERT: B 443 TYR cc_start: 0.7112 (m-80) cc_final: 0.6871 (m-80) REVERT: B 463 LYS cc_start: 0.8377 (tttt) cc_final: 0.8046 (ttpt) REVERT: B 485 MET cc_start: 0.7345 (mtp) cc_final: 0.6948 (mtm) REVERT: B 660 ASP cc_start: 0.7557 (m-30) cc_final: 0.7278 (m-30) REVERT: B 690 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6541 (mm-30) REVERT: B 719 LYS cc_start: 0.7272 (mmtt) cc_final: 0.7006 (mttm) REVERT: F 37 ARG cc_start: 0.7810 (mtt-85) cc_final: 0.7413 (mtt-85) REVERT: F 129 LYS cc_start: 0.8068 (mttt) cc_final: 0.7702 (mtpt) REVERT: F 204 ARG cc_start: 0.7875 (mmt-90) cc_final: 0.7053 (mmm160) outliers start: 36 outliers final: 20 residues processed: 282 average time/residue: 0.7654 time to fit residues: 237.9240 Evaluate side-chains 267 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 612 ASP Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 780 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 1.9990 chunk 161 optimal weight: 0.0270 chunk 96 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 222 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 142 optimal weight: 0.0170 chunk 207 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 232 optimal weight: 2.9990 chunk 165 optimal weight: 6.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.203401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128052 restraints weight = 26357.007| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.09 r_work: 0.3187 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19228 Z= 0.113 Angle : 0.528 10.313 25904 Z= 0.266 Chirality : 0.041 0.336 2852 Planarity : 0.004 0.053 3164 Dihedral : 8.270 72.701 2906 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.30 % Allowed : 18.42 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: 1.59 (0.18), residues: 2312 helix: 2.41 (0.14), residues: 1336 sheet: -1.78 (0.39), residues: 170 loop : -0.64 (0.22), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 706 TYR 0.021 0.001 TYR C 446 PHE 0.013 0.001 PHE C 606 TRP 0.010 0.001 TRP A 788 HIS 0.005 0.001 HIS H 60 Details of bonding type rmsd covalent geometry : bond 0.00252 (19210) covalent geometry : angle 0.52854 (25876) SS BOND : bond 0.00157 ( 14) SS BOND : angle 0.42453 ( 28) hydrogen bonds : bond 0.03921 ( 1067) hydrogen bonds : angle 3.69110 ( 3087) Misc. bond : bond 0.00006 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: H 99 ARG cc_start: 0.7601 (mtm180) cc_final: 0.6532 (mmm160) REVERT: H 129 LYS cc_start: 0.7986 (mttt) cc_final: 0.7605 (mtpt) REVERT: D 423 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6233 (tmt) REVERT: D 429 MET cc_start: 0.5510 (mtp) cc_final: 0.5170 (mtm) REVERT: D 432 LYS cc_start: 0.6373 (pmtt) cc_final: 0.5814 (ttmp) REVERT: D 436 MET cc_start: 0.6280 (mpp) cc_final: 0.5181 (mpt) REVERT: D 656 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: D 660 ASP cc_start: 0.7530 (m-30) cc_final: 0.7237 (m-30) REVERT: D 678 LYS cc_start: 0.7387 (tttt) cc_final: 0.7070 (ttpp) REVERT: D 690 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: D 748 ASN cc_start: 0.8311 (m-40) cc_final: 0.7972 (m-40) REVERT: A 480 LYS cc_start: 0.7082 (mmpt) cc_final: 0.6457 (mmmm) REVERT: A 491 TYR cc_start: 0.7347 (m-10) cc_final: 0.6881 (m-10) REVERT: A 656 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7116 (mm-30) REVERT: G 65 ARG cc_start: 0.7415 (mtm-85) cc_final: 0.7082 (mtm-85) REVERT: G 99 ARG cc_start: 0.7122 (mtt180) cc_final: 0.6277 (mmm160) REVERT: G 131 ARG cc_start: 0.7619 (mtt180) cc_final: 0.6263 (mmm160) REVERT: G 204 ARG cc_start: 0.7184 (tpp80) cc_final: 0.6869 (mpt180) REVERT: E 99 ARG cc_start: 0.7130 (mtt180) cc_final: 0.6316 (mmm160) REVERT: E 131 ARG cc_start: 0.7658 (mtt180) cc_final: 0.6348 (mmm160) REVERT: E 204 ARG cc_start: 0.7195 (tpp80) cc_final: 0.6915 (mpt180) REVERT: C 463 LYS cc_start: 0.7426 (tttt) cc_final: 0.6711 (pmtt) REVERT: C 572 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7642 (mm-30) REVERT: C 685 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7293 (pttt) REVERT: B 422 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7214 (mm) REVERT: B 423 MET cc_start: 0.7204 (OUTLIER) cc_final: 0.6526 (tmt) REVERT: B 429 MET cc_start: 0.5290 (mtp) cc_final: 0.4837 (mtm) REVERT: B 436 MET cc_start: 0.5811 (mpp) cc_final: 0.5126 (mpt) REVERT: B 443 TYR cc_start: 0.7062 (m-80) cc_final: 0.6706 (m-80) REVERT: B 463 LYS cc_start: 0.8378 (tttt) cc_final: 0.8052 (ttpt) REVERT: B 485 MET cc_start: 0.7417 (mtp) cc_final: 0.7059 (mtm) REVERT: B 660 ASP cc_start: 0.7540 (m-30) cc_final: 0.7315 (m-30) REVERT: B 690 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6581 (mm-30) REVERT: B 719 LYS cc_start: 0.7274 (mmtt) cc_final: 0.7042 (mttm) REVERT: F 99 ARG cc_start: 0.7602 (mtm180) cc_final: 0.6521 (mmm160) REVERT: F 129 LYS cc_start: 0.8057 (mttt) cc_final: 0.7690 (mtpt) REVERT: F 204 ARG cc_start: 0.7901 (mmt-90) cc_final: 0.7132 (mmm160) outliers start: 25 outliers final: 17 residues processed: 261 average time/residue: 0.7087 time to fit residues: 205.3651 Evaluate side-chains 259 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 236 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 ILE Chi-restraints excluded: chain D residue 423 MET Chi-restraints excluded: chain D residue 612 ASP Chi-restraints excluded: chain D residue 656 GLU Chi-restraints excluded: chain D residue 690 GLU Chi-restraints excluded: chain D residue 780 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 742 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain C residue 742 THR Chi-restraints excluded: chain C residue 745 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 423 MET Chi-restraints excluded: chain B residue 612 ASP Chi-restraints excluded: chain B residue 690 GLU Chi-restraints excluded: chain B residue 780 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 14 ILE Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain F residue 208 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 120 optimal weight: 0.2980 chunk 6 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 150 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 HIS ** D 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.201539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.122955 restraints weight = 30822.446| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.32 r_work: 0.3107 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19228 Z= 0.124 Angle : 0.535 10.125 25904 Z= 0.269 Chirality : 0.041 0.339 2852 Planarity : 0.004 0.052 3164 Dihedral : 8.237 71.758 2906 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.30 % Allowed : 18.68 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.22 % 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: 1.60 (0.18), residues: 2312 helix: 2.41 (0.14), residues: 1330 sheet: -1.71 (0.39), residues: 170 loop : -0.62 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 706 TYR 0.021 0.001 TYR C 446 PHE 0.013 0.001 PHE C 606 TRP 0.009 0.001 TRP C 788 HIS 0.005 0.001 HIS H 205 Details of bonding type rmsd covalent geometry : bond 0.00282 (19210) covalent geometry : angle 0.53529 (25876) SS BOND : bond 0.00173 ( 14) SS BOND : angle 0.37995 ( 28) hydrogen bonds : bond 0.04022 ( 1067) hydrogen bonds : angle 3.69590 ( 3087) Misc. bond : bond 0.00012 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10386.27 seconds wall clock time: 176 minutes 43.20 seconds (10603.20 seconds total)