Starting phenix.real_space_refine on Fri Jan 17 22:59:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xa0_38190/01_2025/8xa0_38190_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xa0_38190/01_2025/8xa0_38190.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xa0_38190/01_2025/8xa0_38190.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xa0_38190/01_2025/8xa0_38190.map" model { file = "/net/cci-nas-00/data/ceres_data/8xa0_38190/01_2025/8xa0_38190_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xa0_38190/01_2025/8xa0_38190_neut.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 331 5.16 5 C 36220 2.51 5 N 10134 2.21 5 O 10342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 57027 Number of models: 1 Model: "" Number of chains: 13 Chain: "2" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 384 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "A" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 8918 Classifications: {'peptide': 1155} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1078} Chain breaks: 4 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 12, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "C" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 8918 Classifications: {'peptide': 1155} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1078} Chain breaks: 4 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 12, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "E" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 8918 Classifications: {'peptide': 1155} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1078} Chain breaks: 4 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 12, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "F" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 8918 Classifications: {'peptide': 1155} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1078} Chain breaks: 4 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 12, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 8918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1155, 8918 Classifications: {'peptide': 1155} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1078} Chain breaks: 4 Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ARG:plan': 12, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "h" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4206 Classifications: {'peptide': 550} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 509} Chain breaks: 7 Chain: "q" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 766 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 8, 'TRANS': 85} Chain: "u" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 654 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 6, 'TRANS': 73} Chain: "y" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 384 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "R" Number of atoms: 1847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1847 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 20, 'TRANS': 235} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 101 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 49 Chain: "V" Number of atoms: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 1975 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 16, 'TRANS': 246} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "Z" Number of atoms: 2221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2221 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 2 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 42 Time building chain proxies: 24.57, per 1000 atoms: 0.43 Number of scatterers: 57027 At special positions: 0 Unit cell: (230.85, 179.55, 180.9, 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 331 16.00 O 10342 8.00 N 10134 7.00 C 36220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 846 " - pdb=" SG CYS A 985 " distance=2.03 Simple disulfide: pdb=" SG CYS C 846 " - pdb=" SG CYS C 985 " distance=2.03 Simple disulfide: pdb=" SG CYS E 846 " - pdb=" SG CYS E 985 " distance=2.03 Simple disulfide: pdb=" SG CYS F 846 " - pdb=" SG CYS F 985 " distance=2.03 Simple disulfide: pdb=" SG CYS G 846 " - pdb=" SG CYS G 985 " 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=0, symmetry=0 Time building additional restraints: 11.04 Conformation dependent library (CDL) restraints added in 6.2 seconds 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13876 Finding SS restraints... Secondary structure from input PDB file: 266 helices and 69 sheets defined 38.8% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.34 Creating SS restraints... Processing helix chain '2' and resid 3092 through 3138 removed outlier: 3.607A pdb=" N ARG 23096 " --> pdb=" O GLN 23092 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER 23097 " --> pdb=" O ARG 23093 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU 23099 " --> pdb=" O GLY 23095 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA 23100 " --> pdb=" O ARG 23096 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL 23101 " --> pdb=" O SER 23097 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU 23102 " --> pdb=" O ALA 23098 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN 23111 " --> pdb=" O TYR 23107 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU 23121 " --> pdb=" O ARG 23117 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS 23122 " --> pdb=" O ARG 23118 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS 23123 " --> pdb=" O ALA 23119 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA 23126 " --> pdb=" O HIS 23122 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL 23127 " --> pdb=" O HIS 23123 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU 23138 " --> pdb=" O VAL 23134 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.504A pdb=" N ASN A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 203 removed outlier: 3.834A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 216 Proline residue: A 212 - end of helix Processing helix chain 'A' and resid 222 through 241 removed outlier: 3.643A pdb=" N ALA A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 264 removed outlier: 3.905A pdb=" N ILE A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 303 removed outlier: 4.516A pdb=" N GLY A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 473 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.601A pdb=" N CYS A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.509A pdb=" N LEU A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.774A pdb=" N GLN A 495 " --> pdb=" O VAL A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 528 Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.505A pdb=" N LEU A 555 " --> pdb=" O ASN A 552 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 556 " --> pdb=" O PRO A 553 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 558 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.796A pdb=" N ILE A 598 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 removed outlier: 3.525A pdb=" N GLY A 616 " --> pdb=" O GLY A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 635 Processing helix chain 'A' and resid 640 through 651 removed outlier: 4.385A pdb=" N TYR A 644 " --> pdb=" O PRO A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 658 Processing helix chain 'A' and resid 660 through 676 removed outlier: 3.985A pdb=" N GLN A 674 " --> pdb=" O GLY A 670 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N SER A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 693 removed outlier: 4.089A pdb=" N LEU A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET A 688 " --> pdb=" O PHE A 684 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N TYR A 689 " --> pdb=" O HIS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 725 removed outlier: 3.509A pdb=" N ILE A 704 " --> pdb=" O PRO A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 756 through 766 removed outlier: 4.094A pdb=" N ALA A 766 " --> pdb=" O ARG A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 792 Processing helix chain 'A' and resid 822 through 842 removed outlier: 3.908A pdb=" N GLY A 826 " --> pdb=" O ASP A 822 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 837 " --> pdb=" O TYR A 833 " (cutoff:3.500A) Proline residue: A 838 - end of helix Processing helix chain 'A' and resid 851 through 856 Processing helix chain 'A' and resid 857 through 861 removed outlier: 4.076A pdb=" N GLN A 860 " --> pdb=" O PRO A 857 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ALA A 861 " --> pdb=" O ALA A 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 861' Processing helix chain 'A' and resid 893 through 901 removed outlier: 4.101A pdb=" N ALA A 901 " --> pdb=" O TYR A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 912 through 917 Processing helix chain 'A' and resid 934 through 938 removed outlier: 3.829A pdb=" N ALA A 938 " --> pdb=" O ALA A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 Processing helix chain 'A' and resid 996 through 1004 Processing helix chain 'A' and resid 1010 through 1014 removed outlier: 3.763A pdb=" N LEU A1013 " --> pdb=" O PRO A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1032 removed outlier: 3.747A pdb=" N ALA A1026 " --> pdb=" O ARG A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1047 Processing helix chain 'A' and resid 1051 through 1062 Processing helix chain 'A' and resid 1159 through 1172 removed outlier: 3.562A pdb=" N THR A1163 " --> pdb=" O HIS A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1220 removed outlier: 4.135A pdb=" N PHE A1218 " --> pdb=" O ASP A1214 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR A1220 " --> pdb=" O GLN A1216 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1365 Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 148 through 160 removed outlier: 3.515A pdb=" N ASN C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL C 160 " --> pdb=" O SER C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 202 removed outlier: 3.822A pdb=" N PHE C 188 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU C 189 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA C 193 " --> pdb=" O GLU C 189 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP C 194 " --> pdb=" O ARG C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 216 Proline residue: C 212 - end of helix Processing helix chain 'C' and resid 222 through 241 removed outlier: 3.580A pdb=" N ALA C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 251 through 264 removed outlier: 3.836A pdb=" N ILE C 255 " --> pdb=" O GLU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 303 removed outlier: 4.693A pdb=" N GLY C 302 " --> pdb=" O GLN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 477 removed outlier: 3.789A pdb=" N MET C 475 " --> pdb=" O ARG C 472 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY C 476 " --> pdb=" O ASP C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 485 removed outlier: 3.743A pdb=" N LEU C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP C 485 " --> pdb=" O SER C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 494 Processing helix chain 'C' and resid 517 through 528 Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 552 through 556 removed outlier: 3.728A pdb=" N ARG C 556 " --> pdb=" O PRO C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 598 removed outlier: 3.924A pdb=" N ILE C 598 " --> pdb=" O ASN C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 616 Processing helix chain 'C' and resid 623 through 635 Processing helix chain 'C' and resid 641 through 651 Processing helix chain 'C' and resid 653 through 658 Processing helix chain 'C' and resid 660 through 676 removed outlier: 3.924A pdb=" N GLN C 674 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER C 675 " --> pdb=" O TYR C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 693 removed outlier: 3.934A pdb=" N LEU C 687 " --> pdb=" O ASN C 683 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N MET C 688 " --> pdb=" O PHE C 684 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TYR C 689 " --> pdb=" O HIS C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 696 No H-bonds generated for 'chain 'C' and resid 694 through 696' Processing helix chain 'C' and resid 700 through 725 removed outlier: 3.551A pdb=" N ILE C 704 " --> pdb=" O PRO C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 756 through 766 removed outlier: 4.118A pdb=" N ALA C 766 " --> pdb=" O ARG C 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 835 removed outlier: 4.077A pdb=" N GLY C 826 " --> pdb=" O ASP C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 835 through 842 Processing helix chain 'C' and resid 851 through 856 Processing helix chain 'C' and resid 857 through 861 removed outlier: 3.736A pdb=" N GLN C 860 " --> pdb=" O PRO C 857 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA C 861 " --> pdb=" O ALA C 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 857 through 861' Processing helix chain 'C' and resid 893 through 901 removed outlier: 3.969A pdb=" N ALA C 901 " --> pdb=" O TYR C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 912 through 917 Processing helix chain 'C' and resid 934 through 938 removed outlier: 3.847A pdb=" N ALA C 938 " --> pdb=" O ALA C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 992 Processing helix chain 'C' and resid 996 through 1004 removed outlier: 3.593A pdb=" N ARG C1000 " --> pdb=" O THR C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1014 removed outlier: 3.765A pdb=" N LEU C1013 " --> pdb=" O PRO C1010 " (cutoff:3.500A) Processing helix chain 'C' and resid 1022 through 1031 removed outlier: 3.750A pdb=" N ALA C1026 " --> pdb=" O ARG C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1047 Processing helix chain 'C' and resid 1051 through 1062 Processing helix chain 'C' and resid 1159 through 1172 removed outlier: 3.617A pdb=" N THR C1163 " --> pdb=" O HIS C1159 " (cutoff:3.500A) Processing helix chain 'C' and resid 1214 through 1219 Processing helix chain 'C' and resid 1358 through 1365 removed outlier: 3.577A pdb=" N LEU C1362 " --> pdb=" O ASP C1358 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 148 through 160 removed outlier: 3.586A pdb=" N ASN E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL E 160 " --> pdb=" O SER E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 202 removed outlier: 3.896A pdb=" N PHE E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU E 189 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP E 194 " --> pdb=" O ARG E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 209 Processing helix chain 'E' and resid 210 through 216 Processing helix chain 'E' and resid 222 through 241 removed outlier: 3.631A pdb=" N ALA E 226 " --> pdb=" O LEU E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 248 Processing helix chain 'E' and resid 251 through 264 removed outlier: 3.838A pdb=" N ILE E 255 " --> pdb=" O GLU E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 303 removed outlier: 4.655A pdb=" N GLY E 302 " --> pdb=" O GLN E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 479 removed outlier: 3.688A pdb=" N CYS E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 480 through 485 removed outlier: 3.522A pdb=" N LEU E 484 " --> pdb=" O SER E 481 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP E 485 " --> pdb=" O SER E 482 " (cutoff:3.500A) Processing helix chain 'E' and resid 486 through 494 Processing helix chain 'E' and resid 517 through 528 Processing helix chain 'E' and resid 543 through 549 Processing helix chain 'E' and resid 552 through 556 removed outlier: 3.850A pdb=" N ARG E 556 " --> pdb=" O PRO E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 594 through 598 removed outlier: 3.909A pdb=" N ILE E 598 " --> pdb=" O ASN E 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 616 Processing helix chain 'E' and resid 623 through 635 Processing helix chain 'E' and resid 640 through 651 removed outlier: 4.415A pdb=" N TYR E 644 " --> pdb=" O PRO E 640 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 658 Processing helix chain 'E' and resid 660 through 676 removed outlier: 3.991A pdb=" N GLN E 674 " --> pdb=" O GLY E 670 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER E 675 " --> pdb=" O TYR E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 693 removed outlier: 4.455A pdb=" N LEU E 687 " --> pdb=" O ASN E 683 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET E 688 " --> pdb=" O PHE E 684 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N TYR E 689 " --> pdb=" O HIS E 685 " (cutoff:3.500A) Processing helix chain 'E' and resid 694 through 696 No H-bonds generated for 'chain 'E' and resid 694 through 696' Processing helix chain 'E' and resid 700 through 725 removed outlier: 3.543A pdb=" N ILE E 704 " --> pdb=" O PRO E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 735 through 741 Processing helix chain 'E' and resid 756 through 766 removed outlier: 4.107A pdb=" N ALA E 766 " --> pdb=" O ARG E 762 " (cutoff:3.500A) Processing helix chain 'E' and resid 822 through 835 removed outlier: 4.090A pdb=" N GLY E 826 " --> pdb=" O ASP E 822 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 842 Processing helix chain 'E' and resid 851 through 856 Processing helix chain 'E' and resid 857 through 861 removed outlier: 3.906A pdb=" N GLN E 860 " --> pdb=" O PRO E 857 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA E 861 " --> pdb=" O ALA E 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 857 through 861' Processing helix chain 'E' and resid 893 through 901 removed outlier: 4.181A pdb=" N ALA E 901 " --> pdb=" O TYR E 897 " (cutoff:3.500A) Processing helix chain 'E' and resid 906 through 912 Processing helix chain 'E' and resid 912 through 917 Processing helix chain 'E' and resid 934 through 938 removed outlier: 3.801A pdb=" N ALA E 938 " --> pdb=" O ALA E 935 " (cutoff:3.500A) Processing helix chain 'E' and resid 987 through 992 Processing helix chain 'E' and resid 996 through 1004 removed outlier: 3.578A pdb=" N ARG E1000 " --> pdb=" O THR E 996 " (cutoff:3.500A) Processing helix chain 'E' and resid 1010 through 1014 removed outlier: 3.796A pdb=" N LEU E1013 " --> pdb=" O PRO E1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 1022 through 1031 removed outlier: 3.755A pdb=" N ALA E1026 " --> pdb=" O ARG E1022 " (cutoff:3.500A) Processing helix chain 'E' and resid 1036 through 1047 Processing helix chain 'E' and resid 1051 through 1062 Processing helix chain 'E' and resid 1159 through 1172 removed outlier: 3.768A pdb=" N THR E1163 " --> pdb=" O HIS E1159 " (cutoff:3.500A) Processing helix chain 'E' and resid 1214 through 1220 removed outlier: 3.868A pdb=" N THR E1220 " --> pdb=" O TYR E1217 " (cutoff:3.500A) Processing helix chain 'E' and resid 1358 through 1365 removed outlier: 3.525A pdb=" N LEU E1362 " --> pdb=" O ASP E1358 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 Processing helix chain 'F' and resid 148 through 160 removed outlier: 3.677A pdb=" N VAL F 160 " --> pdb=" O SER F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 203 removed outlier: 3.791A pdb=" N PHE F 188 " --> pdb=" O VAL F 184 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU F 189 " --> pdb=" O SER F 185 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP F 194 " --> pdb=" O ARG F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 216 Proline residue: F 212 - end of helix Processing helix chain 'F' and resid 222 through 241 removed outlier: 3.680A pdb=" N ALA F 226 " --> pdb=" O LEU F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 251 through 264 removed outlier: 3.842A pdb=" N ILE F 255 " --> pdb=" O GLU F 251 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 256 " --> pdb=" O PRO F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 303 removed outlier: 4.576A pdb=" N GLY F 302 " --> pdb=" O GLN F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 429 through 433 removed outlier: 3.833A pdb=" N ARG F 433 " --> pdb=" O SER F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 477 removed outlier: 3.689A pdb=" N GLY F 476 " --> pdb=" O ASP F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 480 through 485 removed outlier: 3.666A pdb=" N LEU F 483 " --> pdb=" O HIS F 480 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU F 484 " --> pdb=" O SER F 481 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP F 485 " --> pdb=" O SER F 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 480 through 485' Processing helix chain 'F' and resid 486 through 494 Processing helix chain 'F' and resid 517 through 528 Processing helix chain 'F' and resid 543 through 549 Processing helix chain 'F' and resid 552 through 556 removed outlier: 3.623A pdb=" N ARG F 556 " --> pdb=" O PRO F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 594 through 598 removed outlier: 3.876A pdb=" N ILE F 598 " --> pdb=" O ASN F 595 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 616 Processing helix chain 'F' and resid 623 through 635 Processing helix chain 'F' and resid 641 through 651 Processing helix chain 'F' and resid 653 through 658 Processing helix chain 'F' and resid 660 through 676 removed outlier: 3.964A pdb=" N GLN F 674 " --> pdb=" O GLY F 670 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N SER F 675 " --> pdb=" O TYR F 671 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 694 removed outlier: 3.960A pdb=" N LEU F 687 " --> pdb=" O ASN F 683 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N MET F 688 " --> pdb=" O PHE F 684 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N TYR F 689 " --> pdb=" O HIS F 685 " (cutoff:3.500A) Processing helix chain 'F' and resid 700 through 725 removed outlier: 3.507A pdb=" N ILE F 704 " --> pdb=" O PRO F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 735 through 741 Processing helix chain 'F' and resid 756 through 766 removed outlier: 4.066A pdb=" N ALA F 766 " --> pdb=" O ARG F 762 " (cutoff:3.500A) Processing helix chain 'F' and resid 822 through 842 removed outlier: 3.962A pdb=" N GLY F 826 " --> pdb=" O ASP F 822 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE F 837 " --> pdb=" O TYR F 833 " (cutoff:3.500A) Proline residue: F 838 - end of helix Processing helix chain 'F' and resid 851 through 856 Processing helix chain 'F' and resid 857 through 861 removed outlier: 4.073A pdb=" N GLN F 860 " --> pdb=" O PRO F 857 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA F 861 " --> pdb=" O ALA F 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 857 through 861' Processing helix chain 'F' and resid 893 through 901 removed outlier: 4.059A pdb=" N ALA F 901 " --> pdb=" O TYR F 897 " (cutoff:3.500A) Processing helix chain 'F' and resid 906 through 912 Processing helix chain 'F' and resid 912 through 917 Processing helix chain 'F' and resid 934 through 938 removed outlier: 3.819A pdb=" N ALA F 938 " --> pdb=" O ALA F 935 " (cutoff:3.500A) Processing helix chain 'F' and resid 987 through 992 Processing helix chain 'F' and resid 996 through 1004 Processing helix chain 'F' and resid 1010 through 1014 removed outlier: 3.755A pdb=" N LEU F1013 " --> pdb=" O PRO F1010 " (cutoff:3.500A) Processing helix chain 'F' and resid 1022 through 1031 removed outlier: 3.709A pdb=" N ALA F1026 " --> pdb=" O ARG F1022 " (cutoff:3.500A) Processing helix chain 'F' and resid 1036 through 1047 Processing helix chain 'F' and resid 1051 through 1062 Processing helix chain 'F' and resid 1159 through 1172 removed outlier: 3.778A pdb=" N THR F1163 " --> pdb=" O HIS F1159 " (cutoff:3.500A) Processing helix chain 'F' and resid 1214 through 1219 Processing helix chain 'F' and resid 1358 through 1365 removed outlier: 3.739A pdb=" N LEU F1362 " --> pdb=" O ASP F1358 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG F1363 " --> pdb=" O ALA F1359 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 89 Processing helix chain 'G' and resid 148 through 159 Processing helix chain 'G' and resid 166 through 202 removed outlier: 3.834A pdb=" N PHE G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU G 189 " --> pdb=" O SER G 185 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA G 193 " --> pdb=" O GLU G 189 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP G 194 " --> pdb=" O ARG G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 216 Proline residue: G 212 - end of helix Processing helix chain 'G' and resid 222 through 241 removed outlier: 3.632A pdb=" N ALA G 226 " --> pdb=" O LEU G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 248 Processing helix chain 'G' and resid 251 through 264 removed outlier: 3.971A pdb=" N ILE G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER G 256 " --> pdb=" O PRO G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 303 removed outlier: 4.533A pdb=" N GLY G 302 " --> pdb=" O GLN G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 472 through 477 removed outlier: 3.541A pdb=" N GLY G 476 " --> pdb=" O ASP G 473 " (cutoff:3.500A) Processing helix chain 'G' and resid 480 through 485 removed outlier: 3.815A pdb=" N LEU G 483 " --> pdb=" O HIS G 480 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU G 484 " --> pdb=" O SER G 481 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP G 485 " --> pdb=" O SER G 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 480 through 485' Processing helix chain 'G' and resid 486 through 494 Processing helix chain 'G' and resid 517 through 528 Processing helix chain 'G' and resid 543 through 548 Processing helix chain 'G' and resid 552 through 556 removed outlier: 3.740A pdb=" N ARG G 556 " --> pdb=" O PRO G 553 " (cutoff:3.500A) Processing helix chain 'G' and resid 594 through 598 removed outlier: 3.907A pdb=" N ILE G 598 " --> pdb=" O ASN G 595 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 616 Processing helix chain 'G' and resid 623 through 635 Processing helix chain 'G' and resid 641 through 651 Processing helix chain 'G' and resid 653 through 658 Processing helix chain 'G' and resid 660 through 676 removed outlier: 3.961A pdb=" N GLN G 674 " --> pdb=" O GLY G 670 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N SER G 675 " --> pdb=" O TYR G 671 " (cutoff:3.500A) Processing helix chain 'G' and resid 683 through 693 removed outlier: 3.808A pdb=" N LEU G 687 " --> pdb=" O ASN G 683 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N MET G 688 " --> pdb=" O PHE G 684 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N TYR G 689 " --> pdb=" O HIS G 685 " (cutoff:3.500A) Processing helix chain 'G' and resid 700 through 725 removed outlier: 3.526A pdb=" N ILE G 704 " --> pdb=" O PRO G 700 " (cutoff:3.500A) Processing helix chain 'G' and resid 735 through 741 Processing helix chain 'G' and resid 756 through 766 removed outlier: 4.103A pdb=" N ALA G 766 " --> pdb=" O ARG G 762 " (cutoff:3.500A) Processing helix chain 'G' and resid 822 through 842 removed outlier: 4.143A pdb=" N GLY G 826 " --> pdb=" O ASP G 822 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE G 837 " --> pdb=" O TYR G 833 " (cutoff:3.500A) Proline residue: G 838 - end of helix Processing helix chain 'G' and resid 851 through 856 Processing helix chain 'G' and resid 857 through 861 removed outlier: 4.043A pdb=" N GLN G 860 " --> pdb=" O PRO G 857 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA G 861 " --> pdb=" O ALA G 858 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 857 through 861' Processing helix chain 'G' and resid 893 through 901 removed outlier: 3.984A pdb=" N ALA G 901 " --> pdb=" O TYR G 897 " (cutoff:3.500A) Processing helix chain 'G' and resid 906 through 912 Processing helix chain 'G' and resid 912 through 917 Processing helix chain 'G' and resid 934 through 938 removed outlier: 3.818A pdb=" N ALA G 938 " --> pdb=" O ALA G 935 " (cutoff:3.500A) Processing helix chain 'G' and resid 987 through 992 Processing helix chain 'G' and resid 996 through 1004 Processing helix chain 'G' and resid 1010 through 1014 removed outlier: 3.756A pdb=" N LEU G1013 " --> pdb=" O PRO G1010 " (cutoff:3.500A) Processing helix chain 'G' and resid 1022 through 1031 removed outlier: 3.757A pdb=" N ALA G1026 " --> pdb=" O ARG G1022 " (cutoff:3.500A) Processing helix chain 'G' and resid 1036 through 1047 Processing helix chain 'G' and resid 1051 through 1062 Processing helix chain 'G' and resid 1159 through 1172 removed outlier: 3.701A pdb=" N THR G1163 " --> pdb=" O HIS G1159 " (cutoff:3.500A) Processing helix chain 'G' and resid 1214 through 1220 removed outlier: 4.049A pdb=" N PHE G1218 " --> pdb=" O ASP G1214 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR G1220 " --> pdb=" O GLN G1216 " (cutoff:3.500A) Processing helix chain 'G' and resid 1358 through 1365 removed outlier: 3.535A pdb=" N LEU G1362 " --> pdb=" O ASP G1358 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG G1363 " --> pdb=" O ALA G1359 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 13 removed outlier: 3.975A pdb=" N GLU h 8 " --> pdb=" O HIS h 4 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL h 9 " --> pdb=" O LEU h 5 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN h 10 " --> pdb=" O ALA h 6 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU h 13 " --> pdb=" O VAL h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 37 removed outlier: 3.525A pdb=" N GLY h 37 " --> pdb=" O LEU h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 41 through 45 removed outlier: 3.608A pdb=" N ARG h 45 " --> pdb=" O ALA h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 84 through 91 removed outlier: 3.879A pdb=" N LEU h 89 " --> pdb=" O ALA h 85 " (cutoff:3.500A) Processing helix chain 'h' and resid 139 through 141 No H-bonds generated for 'chain 'h' and resid 139 through 141' Processing helix chain 'h' and resid 149 through 154 Processing helix chain 'h' and resid 159 through 164 Processing helix chain 'h' and resid 165 through 182 removed outlier: 3.639A pdb=" N ARG h 169 " --> pdb=" O THR h 165 " (cutoff:3.500A) Processing helix chain 'h' and resid 183 through 185 No H-bonds generated for 'chain 'h' and resid 183 through 185' Processing helix chain 'h' and resid 186 through 199 removed outlier: 3.513A pdb=" N ALA h 194 " --> pdb=" O LYS h 190 " (cutoff:3.500A) Processing helix chain 'h' and resid 233 through 239 removed outlier: 4.242A pdb=" N GLN h 237 " --> pdb=" O SER h 233 " (cutoff:3.500A) Processing helix chain 'h' and resid 243 through 264 removed outlier: 3.913A pdb=" N VAL h 251 " --> pdb=" O ALA h 247 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER h 252 " --> pdb=" O ALA h 248 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU h 256 " --> pdb=" O SER h 252 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN h 257 " --> pdb=" O ILE h 253 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE h 260 " --> pdb=" O GLU h 256 " (cutoff:3.500A) Processing helix chain 'h' and resid 356 through 369 Processing helix chain 'h' and resid 373 through 378 removed outlier: 3.518A pdb=" N LEU h 377 " --> pdb=" O ARG h 373 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TRP h 378 " --> pdb=" O PRO h 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 373 through 378' Processing helix chain 'h' and resid 379 through 381 No H-bonds generated for 'chain 'h' and resid 379 through 381' Processing helix chain 'h' and resid 420 through 434 removed outlier: 3.951A pdb=" N CYS h 430 " --> pdb=" O LEU h 426 " (cutoff:3.500A) Processing helix chain 'h' and resid 437 through 441 Processing helix chain 'h' and resid 442 through 453 removed outlier: 3.545A pdb=" N GLU h 448 " --> pdb=" O ALA h 444 " (cutoff:3.500A) Processing helix chain 'h' and resid 456 through 461 removed outlier: 3.521A pdb=" N LEU h 460 " --> pdb=" O LEU h 456 " (cutoff:3.500A) Processing helix chain 'h' and resid 473 through 498 Processing helix chain 'h' and resid 513 through 515 No H-bonds generated for 'chain 'h' and resid 513 through 515' Processing helix chain 'h' and resid 516 through 541 removed outlier: 3.509A pdb=" N LEU h 520 " --> pdb=" O GLN h 516 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG h 525 " --> pdb=" O GLY h 521 " (cutoff:3.500A) Proline residue: h 528 - end of helix removed outlier: 3.516A pdb=" N MET h 535 " --> pdb=" O LEU h 531 " (cutoff:3.500A) Processing helix chain 'h' and resid 544 through 548 removed outlier: 3.770A pdb=" N PHE h 547 " --> pdb=" O ASP h 544 " (cutoff:3.500A) Processing helix chain 'h' and resid 549 through 561 removed outlier: 3.660A pdb=" N GLY h 561 " --> pdb=" O ALA h 557 " (cutoff:3.500A) Processing helix chain 'h' and resid 635 through 640 removed outlier: 3.784A pdb=" N TYR h 640 " --> pdb=" O CYS h 637 " (cutoff:3.500A) Processing helix chain 'h' and resid 680 through 691 Processing helix chain 'q' and resid 32 through 36 Processing helix chain 'q' and resid 47 through 74 removed outlier: 3.660A pdb=" N VAL q 52 " --> pdb=" O ALA q 48 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA q 65 " --> pdb=" O ALA q 61 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 94 removed outlier: 3.634A pdb=" N ARG q 85 " --> pdb=" O GLU q 81 " (cutoff:3.500A) Proline residue: q 86 - end of helix removed outlier: 3.547A pdb=" N ILE q 94 " --> pdb=" O ASN q 90 " (cutoff:3.500A) Processing helix chain 'u' and resid 47 through 74 removed outlier: 4.039A pdb=" N GLN u 51 " --> pdb=" O THR u 47 " (cutoff:3.500A) Processing helix chain 'u' and resid 75 through 92 removed outlier: 3.898A pdb=" N ILE u 80 " --> pdb=" O LEU u 76 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU u 81 " --> pdb=" O PRO u 77 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG u 82 " --> pdb=" O VAL u 78 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG u 83 " --> pdb=" O ASP u 79 " (cutoff:3.500A) Proline residue: u 86 - end of helix Processing helix chain 'y' and resid 3094 through 3120 removed outlier: 3.967A pdb=" N LEU y3099 " --> pdb=" O GLY y3095 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ALA y3100 " --> pdb=" O ARG y3096 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N VAL y3101 " --> pdb=" O SER y3097 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU y3102 " --> pdb=" O ALA y3098 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN y3111 " --> pdb=" O TYR y3107 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR y3116 " --> pdb=" O GLN y3112 " (cutoff:3.500A) Processing helix chain 'y' and resid 3120 through 3138 removed outlier: 3.931A pdb=" N SER y3124 " --> pdb=" O LEU y3120 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP y3125 " --> pdb=" O LEU y3121 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA y3126 " --> pdb=" O HIS y3122 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL y3127 " --> pdb=" O HIS y3123 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU y3138 " --> pdb=" O VAL y3134 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 26 removed outlier: 3.847A pdb=" N SER R 22 " --> pdb=" O PRO R 18 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA R 23 " --> pdb=" O ALA R 19 " (cutoff:3.500A) Processing helix chain 'R' and resid 47 through 52 Processing helix chain 'R' and resid 59 through 70 Processing helix chain 'R' and resid 145 through 161 removed outlier: 3.636A pdb=" N LEU R 161 " --> pdb=" O ALA R 157 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 220 removed outlier: 3.518A pdb=" N ASN R 212 " --> pdb=" O MET R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 235 Processing helix chain 'R' and resid 251 through 256 removed outlier: 3.654A pdb=" N ALA R 256 " --> pdb=" O ILE R 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 268 through 287 Processing helix chain 'V' and resid 17 through 27 Processing helix chain 'V' and resid 43 through 47 removed outlier: 3.511A pdb=" N ALA V 47 " --> pdb=" O LEU V 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 43 through 47' Processing helix chain 'V' and resid 47 through 52 removed outlier: 4.042A pdb=" N TYR V 51 " --> pdb=" O ALA V 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR V 52 " --> pdb=" O LEU V 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 47 through 52' Processing helix chain 'V' and resid 59 through 68 Processing helix chain 'V' and resid 145 through 163 Processing helix chain 'V' and resid 195 through 209 Processing helix chain 'V' and resid 210 through 226 Processing helix chain 'V' and resid 270 through 287 removed outlier: 3.708A pdb=" N SER V 274 " --> pdb=" O TYR V 270 " (cutoff:3.500A) Processing helix chain 'Z' and resid 147 through 151 Processing helix chain 'Z' and resid 165 through 179 Processing helix chain 'Z' and resid 198 through 205 Processing helix chain 'Z' and resid 212 through 224 Processing helix chain 'Z' and resid 230 through 248 Processing helix chain 'Z' and resid 300 through 302 No H-bonds generated for 'chain 'Z' and resid 300 through 302' Processing helix chain 'Z' and resid 307 through 311 Processing helix chain 'Z' and resid 350 through 356 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 43 removed outlier: 4.143A pdb=" N GLU A 40 " --> pdb=" O GLN G 108 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN G 108 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE G 107 " --> pdb=" O LYS G 134 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 95 removed outlier: 5.894A pdb=" N ILE A 92 " --> pdb=" O TYR A1092 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N VAL A1094 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR A 94 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 132 through 135 removed outlier: 3.839A pdb=" N ILE A 107 " --> pdb=" O LYS A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 removed outlier: 3.645A pdb=" N VAL A1108 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279 removed outlier: 7.247A pdb=" N LEU A 384 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR A 309 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP A 383 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 394 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY A 287 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N GLU A 395 " --> pdb=" O GLY A 287 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU A 289 " --> pdb=" O GLU A 395 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLU A1080 " --> pdb=" O ALA A1132 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 416 through 422 removed outlier: 4.160A pdb=" N GLN A1074 " --> pdb=" O VAL A1203 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL A1203 " --> pdb=" O GLN A1074 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR A1144 " --> pdb=" O CYS A1204 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N PHE A1206 " --> pdb=" O THR A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 457 through 460 Processing sheet with id=AA8, first strand: chain 'A' and resid 563 through 568 Processing sheet with id=AA9, first strand: chain 'A' and resid 752 through 753 removed outlier: 3.783A pdb=" N SER A 931 " --> pdb=" O ILE A 947 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 846 through 848 Processing sheet with id=AB2, first strand: chain 'A' and resid 1355 through 1356 Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 95 Processing sheet with id=AB4, first strand: chain 'C' and resid 133 through 135 removed outlier: 3.750A pdb=" N ILE C 107 " --> pdb=" O LYS C 134 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 108 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU E 40 " --> pdb=" O GLN C 108 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 146 through 147 removed outlier: 3.561A pdb=" N VAL C1108 " --> pdb=" O ILE C 147 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 305 through 312 removed outlier: 4.935A pdb=" N GLN C 305 " --> pdb=" O ILE C 386 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE C 386 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N LEU C 384 " --> pdb=" O ASP C 307 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR C 309 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ASP C 383 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU C 394 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 387 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU C 289 " --> pdb=" O GLU C 395 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU C1080 " --> pdb=" O ALA C1132 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 416 through 422 removed outlier: 4.290A pdb=" N GLN C1074 " --> pdb=" O VAL C1203 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL C1203 " --> pdb=" O GLN C1074 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR C1144 " --> pdb=" O CYS C1204 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N PHE C1206 " --> pdb=" O THR C1144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 456 through 460 Processing sheet with id=AB9, first strand: chain 'C' and resid 563 through 568 Processing sheet with id=AC1, first strand: chain 'C' and resid 752 through 753 removed outlier: 3.664A pdb=" N SER C 931 " --> pdb=" O ILE C 947 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 956 through 958 removed outlier: 3.751A pdb=" N TYR C 975 " --> pdb=" O GLY C 849 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 1355 through 1356 Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 95 Processing sheet with id=AC5, first strand: chain 'E' and resid 132 through 135 removed outlier: 3.783A pdb=" N ILE E 107 " --> pdb=" O LYS E 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 144 through 147 Processing sheet with id=AC7, first strand: chain 'E' and resid 278 through 279 removed outlier: 4.939A pdb=" N GLN E 305 " --> pdb=" O ILE E 386 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE E 386 " --> pdb=" O GLN E 305 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU E 384 " --> pdb=" O ASP E 307 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR E 309 " --> pdb=" O ALA E 382 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP E 383 " --> pdb=" O LEU E 394 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU E 394 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL E 387 " --> pdb=" O LYS E 390 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLY E 287 " --> pdb=" O PHE E 393 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLU E 395 " --> pdb=" O GLY E 287 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LEU E 289 " --> pdb=" O GLU E 395 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU E1080 " --> pdb=" O ALA E1132 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 416 through 422 removed outlier: 4.114A pdb=" N GLN E1074 " --> pdb=" O VAL E1203 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL E1203 " --> pdb=" O GLN E1074 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N THR E1144 " --> pdb=" O CYS E1204 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N PHE E1206 " --> pdb=" O THR E1144 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 456 through 460 Processing sheet with id=AD1, first strand: chain 'E' and resid 563 through 568 Processing sheet with id=AD2, first strand: chain 'E' and resid 752 through 753 removed outlier: 3.601A pdb=" N SER E 931 " --> pdb=" O ILE E 947 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 956 through 958 removed outlier: 3.666A pdb=" N TYR E 975 " --> pdb=" O GLY E 849 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 1355 through 1356 Processing sheet with id=AD5, first strand: chain 'F' and resid 91 through 95 Processing sheet with id=AD6, first strand: chain 'F' and resid 133 through 135 removed outlier: 3.772A pdb=" N ILE F 107 " --> pdb=" O LYS F 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 146 through 147 removed outlier: 3.566A pdb=" N VAL F1108 " --> pdb=" O ILE F 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 278 through 279 removed outlier: 7.223A pdb=" N LEU F 384 " --> pdb=" O ASP F 307 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N THR F 309 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ASP F 383 " --> pdb=" O LEU F 394 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU F 394 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LEU F 289 " --> pdb=" O GLU F 395 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU F1080 " --> pdb=" O ALA F1132 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 417 through 422 removed outlier: 4.030A pdb=" N GLN F1074 " --> pdb=" O VAL F1203 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL F1203 " --> pdb=" O GLN F1074 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR F1144 " --> pdb=" O CYS F1204 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE F1206 " --> pdb=" O THR F1144 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 456 through 460 Processing sheet with id=AE2, first strand: chain 'F' and resid 563 through 568 Processing sheet with id=AE3, first strand: chain 'F' and resid 752 through 753 removed outlier: 3.556A pdb=" N SER F 931 " --> pdb=" O ILE F 947 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 956 through 958 removed outlier: 3.537A pdb=" N TYR F 975 " --> pdb=" O GLY F 849 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 1355 through 1356 Processing sheet with id=AE6, first strand: chain 'G' and resid 91 through 95 Processing sheet with id=AE7, first strand: chain 'G' and resid 146 through 147 removed outlier: 3.533A pdb=" N VAL G1108 " --> pdb=" O ILE G 147 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 305 through 312 removed outlier: 4.979A pdb=" N GLN G 305 " --> pdb=" O ILE G 386 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE G 386 " --> pdb=" O GLN G 305 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU G 384 " --> pdb=" O ASP G 307 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N THR G 309 " --> pdb=" O ALA G 382 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ASP G 383 " --> pdb=" O LEU G 394 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU G 394 " --> pdb=" O ASP G 383 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL G 387 " --> pdb=" O LYS G 390 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N LEU G 289 " --> pdb=" O GLU G 395 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 416 through 422 removed outlier: 3.721A pdb=" N ILE G 417 " --> pdb=" O ASP G1075 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP G1075 " --> pdb=" O ILE G 417 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN G1074 " --> pdb=" O VAL G1203 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N VAL G1203 " --> pdb=" O GLN G1074 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR G1144 " --> pdb=" O CYS G1204 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N PHE G1206 " --> pdb=" O THR G1144 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 456 through 460 Processing sheet with id=AF2, first strand: chain 'G' and resid 563 through 568 Processing sheet with id=AF3, first strand: chain 'G' and resid 752 through 753 removed outlier: 3.575A pdb=" N SER G 931 " --> pdb=" O ILE G 947 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 956 through 958 removed outlier: 3.622A pdb=" N CYS G 846 " --> pdb=" O MET G 958 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR G 975 " --> pdb=" O GLY G 849 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 1355 through 1356 Processing sheet with id=AF6, first strand: chain 'h' and resid 143 through 146 removed outlier: 3.976A pdb=" N GLN h 61 " --> pdb=" O ALA h 131 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG h 133 " --> pdb=" O GLU h 59 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU h 59 " --> pdb=" O ARG h 133 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N ALA h 135 " --> pdb=" O GLN h 57 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLN h 57 " --> pdb=" O ALA h 135 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE h 77 " --> pdb=" O SER h 113 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER h 113 " --> pdb=" O PHE h 77 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU h 110 " --> pdb=" O ILE h 28 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS h 25 " --> pdb=" O VAL h 400 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL h 400 " --> pdb=" O HIS h 25 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h' and resid 510 through 511 Processing sheet with id=AF8, first strand: chain 'h' and resid 570 through 571 Processing sheet with id=AF9, first strand: chain 'h' and resid 622 through 623 removed outlier: 3.770A pdb=" N VAL h 661 " --> pdb=" O PHE h 669 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE h 669 " --> pdb=" O VAL h 661 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'q' and resid 10 through 13 removed outlier: 3.828A pdb=" N VAL q 12 " --> pdb=" O ARG u 16 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG u 16 " --> pdb=" O VAL q 12 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'R' and resid 40 through 41 removed outlier: 3.910A pdb=" N ALA R 41 " --> pdb=" O GLU R 9 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU R 11 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N LEU R 84 " --> pdb=" O THR R 76 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA R 72 " --> pdb=" O ILE R 88 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 99 through 100 Processing sheet with id=AG4, first strand: chain 'R' and resid 107 through 108 Processing sheet with id=AG5, first strand: chain 'R' and resid 139 through 142 removed outlier: 4.042A pdb=" N LEU R 293 " --> pdb=" O ILE R 113 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'R' and resid 126 through 128 Processing sheet with id=AG7, first strand: chain 'V' and resid 31 through 34 removed outlier: 6.912A pdb=" N LEU V 84 " --> pdb=" O THR V 76 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N VAL V 78 " --> pdb=" O LYS V 82 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS V 82 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ALA V 41 " --> pdb=" O GLU V 7 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU V 9 " --> pdb=" O ALA V 41 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'V' and resid 98 through 100 removed outlier: 3.509A pdb=" N LEU V 293 " --> pdb=" O ILE V 113 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 107 through 108 Processing sheet with id=AH1, first strand: chain 'V' and resid 126 through 128 removed outlier: 3.802A pdb=" N ILE V 126 " --> pdb=" O ILE V 135 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 122 through 127 Processing sheet with id=AH3, first strand: chain 'Z' and resid 195 through 197 removed outlier: 6.701A pdb=" N VAL Z 142 " --> pdb=" O PHE Z 259 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Z' and resid 280 through 281 removed outlier: 6.732A pdb=" N VAL Z 321 " --> pdb=" O ILE Z 436 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR Z 438 " --> pdb=" O LYS Z 319 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS Z 319 " --> pdb=" O THR Z 438 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TRP Z 305 " --> pdb=" O LEU Z 342 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Z' and resid 280 through 281 Processing sheet with id=AH6, first strand: chain 'Z' and resid 451 through 452 2114 hydrogen bonds defined for protein. 5835 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: 24.23 Time building geometry restraints manager: 13.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 19186 1.34 - 1.46: 12541 1.46 - 1.58: 26115 1.58 - 1.70: 3 1.70 - 1.82: 516 Bond restraints: 58361 Sorted by residual: bond pdb=" CG PRO C 535 " pdb=" CD PRO C 535 " ideal model delta sigma weight residual 1.503 1.224 0.279 3.40e-02 8.65e+02 6.75e+01 bond pdb=" CG PRO F 535 " pdb=" CD PRO F 535 " ideal model delta sigma weight residual 1.503 1.250 0.253 3.40e-02 8.65e+02 5.52e+01 bond pdb=" CB PRO C 535 " pdb=" CG PRO C 535 " ideal model delta sigma weight residual 1.492 1.639 -0.147 5.00e-02 4.00e+02 8.63e+00 bond pdb=" CB PRO F 535 " pdb=" CG PRO F 535 " ideal model delta sigma weight residual 1.492 1.625 -0.133 5.00e-02 4.00e+02 7.09e+00 bond pdb=" N PRO C 535 " pdb=" CD PRO C 535 " ideal model delta sigma weight residual 1.473 1.501 -0.028 1.40e-02 5.10e+03 4.02e+00 ... (remaining 58356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 78990 3.15 - 6.30: 498 6.30 - 9.45: 53 9.45 - 12.60: 6 12.60 - 15.75: 4 Bond angle restraints: 79551 Sorted by residual: angle pdb=" N PRO C 535 " pdb=" CD PRO C 535 " pdb=" CG PRO C 535 " ideal model delta sigma weight residual 103.20 87.45 15.75 1.50e+00 4.44e-01 1.10e+02 angle pdb=" CA PRO F 535 " pdb=" N PRO F 535 " pdb=" CD PRO F 535 " ideal model delta sigma weight residual 112.00 97.42 14.58 1.40e+00 5.10e-01 1.09e+02 angle pdb=" CA PRO C 535 " pdb=" N PRO C 535 " pdb=" CD PRO C 535 " ideal model delta sigma weight residual 112.00 97.62 14.38 1.40e+00 5.10e-01 1.06e+02 angle pdb=" N PRO F 535 " pdb=" CD PRO F 535 " pdb=" CG PRO F 535 " ideal model delta sigma weight residual 103.20 88.32 14.88 1.50e+00 4.44e-01 9.84e+01 angle pdb=" C ILE C 420 " pdb=" N MET C 421 " pdb=" CA MET C 421 " ideal model delta sigma weight residual 122.64 132.39 -9.75 1.25e+00 6.40e-01 6.09e+01 ... (remaining 79546 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 32113 18.00 - 36.00: 2443 36.00 - 54.01: 335 54.01 - 72.01: 56 72.01 - 90.01: 42 Dihedral angle restraints: 34989 sinusoidal: 13534 harmonic: 21455 Sorted by residual: dihedral pdb=" CB CYS G 846 " pdb=" SG CYS G 846 " pdb=" SG CYS G 985 " pdb=" CB CYS G 985 " ideal model delta sinusoidal sigma weight residual -86.00 -1.26 -84.74 1 1.00e+01 1.00e-02 8.72e+01 dihedral pdb=" CB CYS C 846 " pdb=" SG CYS C 846 " pdb=" SG CYS C 985 " pdb=" CB CYS C 985 " ideal model delta sinusoidal sigma weight residual -86.00 -2.29 -83.71 1 1.00e+01 1.00e-02 8.55e+01 dihedral pdb=" CB CYS A 846 " pdb=" SG CYS A 846 " pdb=" SG CYS A 985 " pdb=" CB CYS A 985 " ideal model delta sinusoidal sigma weight residual -86.00 -2.41 -83.59 1 1.00e+01 1.00e-02 8.53e+01 ... (remaining 34986 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 5903 0.034 - 0.069: 2173 0.069 - 0.103: 803 0.103 - 0.137: 230 0.137 - 0.171: 32 Chirality restraints: 9141 Sorted by residual: chirality pdb=" CB ILE C 863 " pdb=" CA ILE C 863 " pdb=" CG1 ILE C 863 " pdb=" CG2 ILE C 863 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CA ILE V 53 " pdb=" N ILE V 53 " pdb=" C ILE V 53 " pdb=" CB ILE V 53 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CB ILE F 412 " pdb=" CA ILE F 412 " pdb=" CG1 ILE F 412 " pdb=" CG2 ILE F 412 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 9138 not shown) Planarity restraints: 10399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 534 " 0.083 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO C 535 " -0.197 5.00e-02 4.00e+02 pdb=" CA PRO C 535 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 535 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 534 " 0.082 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO F 535 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO F 535 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO F 535 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 560 " -0.077 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO A 561 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO A 561 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 561 " -0.061 5.00e-02 4.00e+02 ... (remaining 10396 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 746 2.61 - 3.18: 51675 3.18 - 3.76: 90271 3.76 - 4.33: 117836 4.33 - 4.90: 192061 Nonbonded interactions: 452589 Sorted by model distance: nonbonded pdb=" O GLU F 398 " pdb=" NE2 GLN F 403 " model vdw 2.039 3.120 nonbonded pdb=" OD1 ASP C 194 " pdb=" OH TYR C 402 " model vdw 2.058 3.040 nonbonded pdb=" O ALA Z 171 " pdb=" NH2 ARG Z 237 " model vdw 2.073 3.120 nonbonded pdb=" OD1 ASP G 194 " pdb=" OH TYR G 402 " model vdw 2.081 3.040 nonbonded pdb=" NH1 ARG G1219 " pdb=" OE1 GLU G1374 " model vdw 2.117 3.120 ... (remaining 452584 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 '2' selection = chain 'y' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = (chain 'q' and resid 13 through 92) selection = chain 'u' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.760 Check model and map are aligned: 0.350 Set scattering table: 0.400 Process input model: 101.820 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.270 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: 0.020 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5023 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 0.279 58361 Z= 0.228 Angle : 0.717 15.747 79551 Z= 0.391 Chirality : 0.043 0.171 9141 Planarity : 0.005 0.114 10399 Dihedral : 12.945 90.011 21098 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.91 % Favored : 92.73 % Rotamer: Outliers : 0.02 % Allowed : 0.25 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.10), residues: 7304 helix: 0.20 (0.11), residues: 2367 sheet: -0.84 (0.16), residues: 1113 loop : -1.42 (0.10), residues: 3824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP R 276 HIS 0.010 0.001 HIS R 39 PHE 0.030 0.001 PHE G 523 TYR 0.024 0.001 TYR Z 226 ARG 0.012 0.001 ARG E1219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 822 time to evaluate : 4.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.7679 (tmm) cc_final: 0.7315 (ttt) REVERT: A 1064 HIS cc_start: 0.3403 (t-90) cc_final: 0.2869 (t-90) REVERT: A 1150 PHE cc_start: 0.4689 (m-80) cc_final: 0.4216 (t80) REVERT: A 1207 VAL cc_start: 0.6385 (t) cc_final: 0.6087 (t) REVERT: A 1361 MET cc_start: 0.5345 (mpp) cc_final: 0.4812 (mpp) REVERT: C 1099 VAL cc_start: 0.7694 (p) cc_final: 0.7484 (m) REVERT: C 1157 MET cc_start: -0.0021 (mtt) cc_final: -0.1250 (tpp) REVERT: C 1189 ARG cc_start: 0.3543 (mmt180) cc_final: 0.2666 (mtm180) REVERT: C 1207 VAL cc_start: 0.7054 (t) cc_final: 0.6821 (t) REVERT: E 241 ASP cc_start: 0.6311 (m-30) cc_final: 0.4748 (m-30) REVERT: E 530 MET cc_start: 0.0400 (ptp) cc_final: -0.0642 (ppp) REVERT: E 1189 ARG cc_start: 0.3283 (mmt180) cc_final: 0.2286 (mtm180) REVERT: F 241 ASP cc_start: 0.6468 (m-30) cc_final: 0.4206 (m-30) REVERT: F 431 MET cc_start: 0.5639 (mmp) cc_final: 0.5362 (mmt) REVERT: F 530 MET cc_start: 0.0423 (ppp) cc_final: 0.0132 (ppp) REVERT: F 917 MET cc_start: 0.3355 (tmm) cc_final: 0.2976 (ttp) REVERT: F 1150 PHE cc_start: 0.4692 (m-80) cc_final: 0.3551 (t80) REVERT: F 1189 ARG cc_start: 0.2672 (mmt-90) cc_final: 0.1558 (mtm180) REVERT: G 1157 MET cc_start: -0.0697 (mtt) cc_final: -0.1897 (tpp) REVERT: G 1189 ARG cc_start: 0.3683 (mmt180) cc_final: 0.3400 (mmp-170) REVERT: h 688 VAL cc_start: 0.6310 (t) cc_final: 0.6009 (m) REVERT: V 101 ASN cc_start: 0.7756 (t0) cc_final: 0.7481 (t0) REVERT: V 282 ARG cc_start: 0.6185 (mtm110) cc_final: 0.5918 (mtm180) REVERT: Z 307 VAL cc_start: 0.6920 (m) cc_final: 0.6642 (p) outliers start: 1 outliers final: 0 residues processed: 823 average time/residue: 0.5388 time to fit residues: 753.2957 Evaluate side-chains 648 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 648 time to evaluate : 4.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 619 optimal weight: 9.9990 chunk 556 optimal weight: 6.9990 chunk 308 optimal weight: 7.9990 chunk 190 optimal weight: 8.9990 chunk 375 optimal weight: 40.0000 chunk 297 optimal weight: 8.9990 chunk 575 optimal weight: 10.0000 chunk 222 optimal weight: 40.0000 chunk 349 optimal weight: 10.0000 chunk 428 optimal weight: 10.0000 chunk 666 optimal weight: 20.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 GLN ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN A1100 HIS C 267 GLN ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 HIS C 651 HIS ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 820 HIS ** C 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1058 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1100 HIS ** C1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 GLN ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 651 HIS E 793 ASN E 820 HIS E1100 HIS E1114 GLN F 108 GLN F 130 ASN ** F 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 792 HIS ** F 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS ** F1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1100 HIS F1114 GLN ** G 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 403 GLN ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 793 ASN G 820 HIS ** G1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 195 HIS h 390 HIS ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 348 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.193870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.177874 restraints weight = 276725.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.177018 restraints weight = 309003.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.177551 restraints weight = 227766.009| |-----------------------------------------------------------------------------| r_work (final): 0.4573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5348 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 58361 Z= 0.229 Angle : 0.681 12.751 79551 Z= 0.343 Chirality : 0.045 0.379 9141 Planarity : 0.006 0.072 10399 Dihedral : 4.781 28.795 8089 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.74 % Favored : 91.92 % Rotamer: Outliers : 1.48 % Allowed : 9.09 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.10), residues: 7304 helix: 0.23 (0.11), residues: 2357 sheet: -1.00 (0.15), residues: 1085 loop : -1.60 (0.10), residues: 3862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 276 HIS 0.011 0.001 HIS C 685 PHE 0.032 0.002 PHE V 137 TYR 0.040 0.002 TYR Z 226 ARG 0.008 0.001 ARG F1087 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 749 time to evaluate : 4.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.8115 (tmm) cc_final: 0.7627 (tmm) REVERT: A 475 MET cc_start: 0.6897 (mpp) cc_final: 0.6654 (mpp) REVERT: A 530 MET cc_start: -0.0389 (ppp) cc_final: -0.0643 (ppp) REVERT: A 958 MET cc_start: 0.4853 (mmp) cc_final: 0.3597 (mtm) REVERT: A 1064 HIS cc_start: 0.3963 (t-90) cc_final: 0.3259 (t-90) REVERT: A 1150 PHE cc_start: 0.5144 (m-80) cc_final: 0.4203 (t80) REVERT: A 1189 ARG cc_start: 0.0503 (mpp-170) cc_final: 0.0231 (mtm180) REVERT: C 115 MET cc_start: 0.6788 (pmm) cc_final: 0.5819 (ptm) REVERT: C 431 MET cc_start: 0.5189 (mmt) cc_final: 0.4982 (mmt) REVERT: C 520 MET cc_start: 0.3381 (ptt) cc_final: 0.2613 (ptt) REVERT: C 1157 MET cc_start: 0.0285 (mtt) cc_final: -0.1372 (tpp) REVERT: C 1189 ARG cc_start: 0.3329 (mmt180) cc_final: 0.2574 (mtm180) REVERT: E 520 MET cc_start: 0.2978 (ptt) cc_final: 0.2659 (ptt) REVERT: E 526 THR cc_start: 0.7524 (m) cc_final: 0.7271 (p) REVERT: E 530 MET cc_start: 0.0598 (ptp) cc_final: -0.0252 (ppp) REVERT: E 1189 ARG cc_start: 0.3107 (mmt180) cc_final: 0.2275 (mtm180) REVERT: F 25 ILE cc_start: 0.3938 (pt) cc_final: 0.3732 (pt) REVERT: F 399 ARG cc_start: 0.7917 (mmp-170) cc_final: 0.6874 (mmm160) REVERT: F 421 MET cc_start: 0.6300 (mmt) cc_final: 0.5566 (mmt) REVERT: F 431 MET cc_start: 0.5352 (mmp) cc_final: 0.5150 (mmp) REVERT: F 530 MET cc_start: 0.0754 (ppp) cc_final: 0.0341 (ppp) REVERT: F 917 MET cc_start: 0.3383 (tmm) cc_final: 0.3038 (ttp) REVERT: F 1189 ARG cc_start: 0.2899 (mmt-90) cc_final: 0.1964 (mtm180) REVERT: G 87 LEU cc_start: 0.7918 (tp) cc_final: 0.7614 (tt) REVERT: G 286 ASP cc_start: 0.5419 (m-30) cc_final: 0.5171 (m-30) REVERT: G 530 MET cc_start: 0.1937 (ppp) cc_final: 0.1658 (ppp) REVERT: G 686 MET cc_start: 0.5841 (ptm) cc_final: 0.5505 (ptp) REVERT: G 1157 MET cc_start: -0.0304 (mtt) cc_final: -0.1850 (tpp) REVERT: G 1189 ARG cc_start: 0.3782 (mmt180) cc_final: 0.3385 (mmp-170) REVERT: h 174 LEU cc_start: 0.4321 (tt) cc_final: 0.4115 (tt) REVERT: u 71 MET cc_start: 0.7325 (mtm) cc_final: 0.7029 (mtm) REVERT: V 65 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7723 (tm-30) REVERT: V 69 MET cc_start: 0.8434 (tpt) cc_final: 0.8183 (tpt) REVERT: Z 219 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7652 (tpp80) REVERT: Z 231 MET cc_start: 0.8099 (mpp) cc_final: 0.6733 (mtm) outliers start: 89 outliers final: 57 residues processed: 783 average time/residue: 0.5359 time to fit residues: 713.9968 Evaluate side-chains 729 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 672 time to evaluate : 4.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 997 ASN Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 1108 VAL Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1207 VAL Chi-restraints excluded: chain E residue 1216 GLN Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 415 ILE Chi-restraints excluded: chain F residue 944 ASN Chi-restraints excluded: chain F residue 1207 VAL Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 423 MET Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 518 VAL Chi-restraints excluded: chain G residue 997 ASN Chi-restraints excluded: chain G residue 1071 VAL Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain Z residue 238 PHE Chi-restraints excluded: chain Z residue 305 TRP Chi-restraints excluded: chain Z residue 321 VAL Chi-restraints excluded: chain Z residue 323 LEU Chi-restraints excluded: chain Z residue 473 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 646 optimal weight: 7.9990 chunk 92 optimal weight: 0.3980 chunk 607 optimal weight: 0.9980 chunk 266 optimal weight: 0.8980 chunk 204 optimal weight: 40.0000 chunk 125 optimal weight: 50.0000 chunk 174 optimal weight: 7.9990 chunk 275 optimal weight: 0.0980 chunk 111 optimal weight: 8.9990 chunk 381 optimal weight: 40.0000 chunk 583 optimal weight: 30.0000 overall best weight: 2.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 23132 HIS A 267 GLN ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 GLN ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 820 HIS ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 GLN E 820 HIS E 980 ASN E1037 ASN ** F 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS ** F 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F1037 ASN ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 740 ASN G 793 ASN G 820 HIS G1102 HIS h 195 HIS h 533 ASN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 320 HIS Z 348 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.195286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.179197 restraints weight = 275829.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.178179 restraints weight = 321155.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.178662 restraints weight = 236539.090| |-----------------------------------------------------------------------------| r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5292 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 58361 Z= 0.162 Angle : 0.624 12.872 79551 Z= 0.308 Chirality : 0.043 0.320 9141 Planarity : 0.005 0.061 10399 Dihedral : 4.522 26.057 8089 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.01 % Favored : 92.65 % Rotamer: Outliers : 1.66 % Allowed : 11.96 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.10), residues: 7304 helix: 0.42 (0.11), residues: 2363 sheet: -1.07 (0.16), residues: 976 loop : -1.52 (0.10), residues: 3965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 276 HIS 0.010 0.001 HIS h 389 PHE 0.040 0.001 PHE F 244 TYR 0.035 0.001 TYR Z 226 ARG 0.006 0.000 ARG R 282 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 734 time to evaluate : 4.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.8093 (tp) cc_final: 0.7836 (tt) REVERT: A 423 MET cc_start: 0.7922 (tmm) cc_final: 0.7621 (ttt) REVERT: A 483 LEU cc_start: 0.4801 (mm) cc_final: 0.4560 (pt) REVERT: A 520 MET cc_start: 0.3563 (ptt) cc_final: 0.3293 (ptt) REVERT: A 530 MET cc_start: 0.0221 (ppp) cc_final: -0.0301 (ppp) REVERT: A 1064 HIS cc_start: 0.3781 (t-90) cc_final: 0.3183 (t-90) REVERT: A 1150 PHE cc_start: 0.4869 (m-80) cc_final: 0.4212 (t80) REVERT: A 1189 ARG cc_start: 0.0316 (mpp-170) cc_final: 0.0105 (mtm180) REVERT: C 115 MET cc_start: 0.6973 (pmm) cc_final: 0.5989 (ptm) REVERT: C 431 MET cc_start: 0.5166 (mmt) cc_final: 0.4966 (mmt) REVERT: C 520 MET cc_start: 0.3322 (ptt) cc_final: 0.2992 (ptt) REVERT: C 958 MET cc_start: 0.2556 (ptt) cc_final: 0.1798 (ptt) REVERT: C 959 MET cc_start: -0.1251 (pmm) cc_final: -0.1536 (pmm) REVERT: C 1157 MET cc_start: -0.0068 (mtt) cc_final: -0.1479 (tpp) REVERT: C 1189 ARG cc_start: 0.3496 (mmt180) cc_final: 0.2638 (mtm180) REVERT: E 520 MET cc_start: 0.3240 (ptt) cc_final: 0.2931 (ptt) REVERT: E 526 THR cc_start: 0.7452 (m) cc_final: 0.7190 (p) REVERT: E 530 MET cc_start: 0.0659 (ptp) cc_final: -0.0193 (ppp) REVERT: E 1189 ARG cc_start: 0.3062 (mmt180) cc_final: 0.2237 (mtm180) REVERT: F 421 MET cc_start: 0.5822 (mmt) cc_final: 0.5353 (mmt) REVERT: F 530 MET cc_start: 0.0729 (ppp) cc_final: 0.0323 (ppp) REVERT: F 917 MET cc_start: 0.3385 (tmm) cc_final: 0.3096 (ttp) REVERT: F 1189 ARG cc_start: 0.2845 (mmt-90) cc_final: 0.1917 (mtm180) REVERT: G 255 ILE cc_start: 0.7775 (mm) cc_final: 0.7351 (mm) REVERT: G 920 MET cc_start: -0.0759 (tmm) cc_final: -0.1504 (tmm) REVERT: G 1157 MET cc_start: -0.0618 (mtt) cc_final: -0.1850 (tpp) REVERT: G 1189 ARG cc_start: 0.3829 (mmt180) cc_final: 0.3516 (mmp-170) REVERT: h 546 PHE cc_start: 0.6464 (t80) cc_final: 0.5913 (p90) REVERT: h 688 VAL cc_start: 0.5760 (t) cc_final: 0.5387 (m) REVERT: R 70 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8044 (ttp80) REVERT: V 69 MET cc_start: 0.8260 (tpt) cc_final: 0.7882 (tpt) REVERT: Z 231 MET cc_start: 0.8083 (mpp) cc_final: 0.6573 (mtm) outliers start: 100 outliers final: 59 residues processed: 770 average time/residue: 0.5711 time to fit residues: 751.9713 Evaluate side-chains 733 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 673 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 997 ASN Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 423 MET Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 1082 LEU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 423 MET Chi-restraints excluded: chain F residue 792 HIS Chi-restraints excluded: chain F residue 944 ASN Chi-restraints excluded: chain F residue 1209 MET Chi-restraints excluded: chain F residue 1217 TYR Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 423 MET Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 793 ASN Chi-restraints excluded: chain G residue 997 ASN Chi-restraints excluded: chain G residue 1071 VAL Chi-restraints excluded: chain G residue 1209 MET Chi-restraints excluded: chain G residue 1375 VAL Chi-restraints excluded: chain h residue 610 MET Chi-restraints excluded: chain y residue 3136 MET Chi-restraints excluded: chain R residue 70 ARG Chi-restraints excluded: chain V residue 15 GLU Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 310 THR Chi-restraints excluded: chain Z residue 238 PHE Chi-restraints excluded: chain Z residue 272 CYS Chi-restraints excluded: chain Z residue 283 GLU Chi-restraints excluded: chain Z residue 299 ILE Chi-restraints excluded: chain Z residue 305 TRP Chi-restraints excluded: chain Z residue 323 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 515 optimal weight: 30.0000 chunk 231 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 375 optimal weight: 20.0000 chunk 423 optimal weight: 30.0000 chunk 560 optimal weight: 20.0000 chunk 528 optimal weight: 5.9990 chunk 439 optimal weight: 9.9990 chunk 686 optimal weight: 3.9990 chunk 591 optimal weight: 7.9990 chunk 199 optimal weight: 40.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 HIS ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 HIS C 685 HIS C 740 ASN C 820 HIS ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 793 ASN E 820 HIS ** E 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN ** F 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 740 ASN ** F 793 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS ** F 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 820 HIS G1102 HIS h 15 HIS ** h 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 195 HIS h 237 GLN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 320 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.192926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.177241 restraints weight = 277182.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.176377 restraints weight = 320810.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.176856 restraints weight = 237474.923| |-----------------------------------------------------------------------------| r_work (final): 0.4565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5283 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 58361 Z= 0.195 Angle : 0.624 14.244 79551 Z= 0.312 Chirality : 0.043 0.335 9141 Planarity : 0.005 0.058 10399 Dihedral : 4.559 25.075 8089 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.75 % Favored : 91.95 % Rotamer: Outliers : 2.77 % Allowed : 13.34 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.10), residues: 7304 helix: 0.40 (0.11), residues: 2377 sheet: -1.05 (0.16), residues: 1042 loop : -1.58 (0.10), residues: 3885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 276 HIS 0.013 0.001 HIS G 792 PHE 0.031 0.002 PHE F 244 TYR 0.027 0.001 TYR Z 226 ARG 0.013 0.000 ARG Z 132 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 695 time to evaluate : 4.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 MET cc_start: 0.7780 (tmm) cc_final: 0.7297 (ttt) REVERT: A 520 MET cc_start: 0.4142 (ptt) cc_final: 0.3715 (ptt) REVERT: A 530 MET cc_start: -0.0594 (ppp) cc_final: -0.0816 (ppp) REVERT: A 686 MET cc_start: 0.5480 (pmm) cc_final: 0.5075 (pmm) REVERT: A 958 MET cc_start: 0.4662 (mmp) cc_final: 0.3574 (mtm) REVERT: A 1064 HIS cc_start: 0.4103 (t-90) cc_final: 0.3111 (t-90) REVERT: A 1150 PHE cc_start: 0.4705 (m-80) cc_final: 0.4192 (t80) REVERT: A 1189 ARG cc_start: 0.1091 (mpp-170) cc_final: 0.0793 (mtm180) REVERT: C 115 MET cc_start: 0.7063 (pmm) cc_final: 0.6163 (ptm) REVERT: C 431 MET cc_start: 0.5580 (mmt) cc_final: 0.5318 (mmt) REVERT: C 520 MET cc_start: 0.3518 (ptt) cc_final: 0.3196 (ptt) REVERT: C 530 MET cc_start: 0.0876 (ppp) cc_final: -0.1318 (ptm) REVERT: C 531 MET cc_start: -0.4254 (mmp) cc_final: -0.4565 (mmp) REVERT: C 789 MET cc_start: 0.1667 (mmm) cc_final: 0.1388 (mmt) REVERT: C 959 MET cc_start: -0.0996 (pmm) cc_final: -0.1382 (pmm) REVERT: C 1157 MET cc_start: 0.0287 (mtt) cc_final: -0.1426 (tpp) REVERT: C 1189 ARG cc_start: 0.3709 (mmt180) cc_final: 0.2793 (mtm180) REVERT: E 520 MET cc_start: 0.3478 (ptt) cc_final: 0.3180 (ptt) REVERT: E 526 THR cc_start: 0.7482 (m) cc_final: 0.7217 (p) REVERT: E 530 MET cc_start: 0.0805 (ptp) cc_final: -0.0150 (ppp) REVERT: E 789 MET cc_start: 0.1232 (mmm) cc_final: 0.0863 (mmt) REVERT: E 1189 ARG cc_start: 0.3258 (mmt180) cc_final: 0.2363 (mtm180) REVERT: F 421 MET cc_start: 0.5725 (OUTLIER) cc_final: 0.5117 (mmt) REVERT: F 431 MET cc_start: 0.5206 (mmp) cc_final: 0.4988 (mmp) REVERT: F 530 MET cc_start: 0.0987 (ppp) cc_final: 0.0782 (ppp) REVERT: F 1157 MET cc_start: 0.0432 (mtt) cc_final: -0.1284 (tpp) REVERT: F 1189 ARG cc_start: 0.3934 (mmt-90) cc_final: 0.2955 (mtm180) REVERT: G 115 MET cc_start: 0.6733 (pmm) cc_final: 0.6164 (ptm) REVERT: G 255 ILE cc_start: 0.7514 (mm) cc_final: 0.7229 (mm) REVERT: G 306 ILE cc_start: 0.8043 (OUTLIER) cc_final: 0.7715 (tt) REVERT: G 530 MET cc_start: 0.0021 (ppp) cc_final: -0.0276 (ppp) REVERT: G 1157 MET cc_start: -0.0391 (mtt) cc_final: -0.2010 (tpp) REVERT: G 1189 ARG cc_start: 0.4135 (mmt180) cc_final: 0.3700 (mmp-170) REVERT: h 174 LEU cc_start: 0.4561 (tt) cc_final: 0.4243 (tt) REVERT: h 511 ASP cc_start: 0.4904 (t70) cc_final: 0.4642 (t70) REVERT: h 546 PHE cc_start: 0.6540 (t80) cc_final: 0.6063 (p90) REVERT: h 688 VAL cc_start: 0.5775 (t) cc_final: 0.5460 (m) REVERT: R 70 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7173 (tmm160) REVERT: V 190 LEU cc_start: 0.6150 (mt) cc_final: 0.5883 (mm) outliers start: 167 outliers final: 115 residues processed: 779 average time/residue: 0.5296 time to fit residues: 705.0081 Evaluate side-chains 772 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 654 time to evaluate : 4.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 997 ASN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1123 VAL Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain C residue 1354 LEU Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 417 ILE Chi-restraints excluded: chain E residue 423 MET Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1216 GLN Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 423 MET Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 622 MET Chi-restraints excluded: chain F residue 792 HIS Chi-restraints excluded: chain F residue 864 VAL Chi-restraints excluded: chain F residue 920 MET Chi-restraints excluded: chain F residue 944 ASN Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1207 VAL Chi-restraints excluded: chain F residue 1209 MET Chi-restraints excluded: chain F residue 1212 SER Chi-restraints excluded: chain F residue 1217 TYR Chi-restraints excluded: chain F residue 1362 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 209 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 423 MET Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 686 MET Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 997 ASN Chi-restraints excluded: chain G residue 1071 VAL Chi-restraints excluded: chain G residue 1072 VAL Chi-restraints excluded: chain G residue 1207 VAL Chi-restraints excluded: chain G residue 1209 MET Chi-restraints excluded: chain G residue 1375 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 555 VAL Chi-restraints excluded: chain h residue 610 MET Chi-restraints excluded: chain y residue 3136 MET Chi-restraints excluded: chain R residue 70 ARG Chi-restraints excluded: chain V residue 37 LEU Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 302 SER Chi-restraints excluded: chain V residue 310 THR Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 238 PHE Chi-restraints excluded: chain Z residue 263 LEU Chi-restraints excluded: chain Z residue 272 CYS Chi-restraints excluded: chain Z residue 299 ILE Chi-restraints excluded: chain Z residue 305 TRP Chi-restraints excluded: chain Z residue 321 VAL Chi-restraints excluded: chain Z residue 323 LEU Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 473 THR Chi-restraints excluded: chain Z residue 475 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 291 optimal weight: 50.0000 chunk 227 optimal weight: 30.0000 chunk 308 optimal weight: 0.6980 chunk 615 optimal weight: 30.0000 chunk 512 optimal weight: 5.9990 chunk 84 optimal weight: 40.0000 chunk 554 optimal weight: 20.0000 chunk 264 optimal weight: 0.0980 chunk 272 optimal weight: 5.9990 chunk 339 optimal weight: 50.0000 chunk 610 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 HIS ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 HIS ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 HIS A 793 ASN ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 820 HIS E 248 HIS ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 682 ASN E 740 ASN E 820 HIS ** E 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS ** F 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 820 HIS G1102 HIS G1379 GLN h 195 HIS ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 320 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.193411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.174503 restraints weight = 192037.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.174079 restraints weight = 182006.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.173791 restraints weight = 185050.752| |-----------------------------------------------------------------------------| r_work (final): 0.4590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5353 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 58361 Z= 0.166 Angle : 0.611 17.222 79551 Z= 0.301 Chirality : 0.043 0.343 9141 Planarity : 0.005 0.056 10399 Dihedral : 4.441 24.054 8089 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.25 % Allowed : 7.35 % Favored : 92.40 % Rotamer: Outliers : 2.56 % Allowed : 14.80 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.10), residues: 7304 helix: 0.55 (0.11), residues: 2330 sheet: -0.97 (0.16), residues: 977 loop : -1.50 (0.10), residues: 3997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 276 HIS 0.012 0.001 HIS C1064 PHE 0.027 0.001 PHE F 244 TYR 0.017 0.001 TYR V 184 ARG 0.009 0.000 ARG Z 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 864 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 710 time to evaluate : 4.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.4371 (mmp) cc_final: 0.3853 (mmt) REVERT: A 530 MET cc_start: 0.0301 (ppp) cc_final: -0.0202 (ppp) REVERT: A 686 MET cc_start: 0.5778 (pmm) cc_final: 0.5356 (pmm) REVERT: A 958 MET cc_start: 0.4403 (mmp) cc_final: 0.2584 (mtm) REVERT: A 1150 PHE cc_start: 0.4780 (m-80) cc_final: 0.4322 (t80) REVERT: C 115 MET cc_start: 0.6782 (pmm) cc_final: 0.6366 (ptm) REVERT: C 196 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8372 (tt) REVERT: C 431 MET cc_start: 0.6311 (mmt) cc_final: 0.5989 (mmt) REVERT: C 789 MET cc_start: 0.1381 (mmm) cc_final: 0.1021 (mmt) REVERT: C 959 MET cc_start: -0.0971 (pmm) cc_final: -0.1216 (pmm) REVERT: C 1157 MET cc_start: 0.0141 (mtt) cc_final: -0.1349 (tpp) REVERT: C 1189 ARG cc_start: 0.3334 (mmt180) cc_final: 0.2488 (mtm180) REVERT: E 520 MET cc_start: 0.2937 (ptt) cc_final: 0.2645 (ptt) REVERT: E 1189 ARG cc_start: 0.3291 (mmt180) cc_final: 0.2585 (mtm180) REVERT: F 421 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5310 (mmt) REVERT: F 530 MET cc_start: 0.1858 (ppp) cc_final: 0.1559 (ppp) REVERT: F 1157 MET cc_start: 0.0035 (mtt) cc_final: -0.1618 (tpp) REVERT: F 1189 ARG cc_start: 0.4193 (mmt-90) cc_final: 0.3088 (mtm180) REVERT: F 1361 MET cc_start: 0.4780 (mpp) cc_final: 0.4037 (mpp) REVERT: G 115 MET cc_start: 0.7044 (pmm) cc_final: 0.6730 (ptm) REVERT: G 255 ILE cc_start: 0.7708 (mm) cc_final: 0.7426 (mm) REVERT: G 306 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7857 (tt) REVERT: G 530 MET cc_start: 0.1561 (ppp) cc_final: 0.1134 (ppp) REVERT: G 686 MET cc_start: 0.5848 (ptm) cc_final: 0.5570 (ptp) REVERT: G 1157 MET cc_start: -0.0638 (mtt) cc_final: -0.2294 (tpp) REVERT: G 1189 ARG cc_start: 0.3776 (mmt180) cc_final: 0.3274 (mmp-170) REVERT: G 1362 LEU cc_start: 0.7604 (tp) cc_final: 0.7391 (tt) REVERT: h 169 ARG cc_start: 0.6051 (ptp90) cc_final: 0.4713 (mtm110) REVERT: h 174 LEU cc_start: 0.4574 (tt) cc_final: 0.4253 (tt) REVERT: R 70 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7835 (ttp80) REVERT: V 69 MET cc_start: 0.8579 (tpt) cc_final: 0.8372 (tpt) REVERT: V 190 LEU cc_start: 0.6392 (mt) cc_final: 0.6152 (mm) REVERT: Z 219 ARG cc_start: 0.8362 (tpp80) cc_final: 0.7802 (tpp-160) outliers start: 154 outliers final: 113 residues processed: 782 average time/residue: 0.5330 time to fit residues: 712.0623 Evaluate side-chains 782 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 665 time to evaluate : 4.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 997 ASN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain C residue 1354 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 423 MET Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 1082 LEU Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1216 GLN Chi-restraints excluded: chain E residue 1217 TYR Chi-restraints excluded: chain E residue 1362 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 421 MET Chi-restraints excluded: chain F residue 423 MET Chi-restraints excluded: chain F residue 792 HIS Chi-restraints excluded: chain F residue 864 VAL Chi-restraints excluded: chain F residue 920 MET Chi-restraints excluded: chain F residue 944 ASN Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1082 LEU Chi-restraints excluded: chain F residue 1099 VAL Chi-restraints excluded: chain F residue 1209 MET Chi-restraints excluded: chain F residue 1217 TYR Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 423 MET Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 997 ASN Chi-restraints excluded: chain G residue 1071 VAL Chi-restraints excluded: chain G residue 1209 MET Chi-restraints excluded: chain G residue 1217 TYR Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 476 VAL Chi-restraints excluded: chain h residue 610 MET Chi-restraints excluded: chain u residue 55 LEU Chi-restraints excluded: chain u residue 71 MET Chi-restraints excluded: chain y residue 3136 MET Chi-restraints excluded: chain R residue 70 ARG Chi-restraints excluded: chain V residue 15 GLU Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 302 SER Chi-restraints excluded: chain V residue 310 THR Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 238 PHE Chi-restraints excluded: chain Z residue 272 CYS Chi-restraints excluded: chain Z residue 305 TRP Chi-restraints excluded: chain Z residue 321 VAL Chi-restraints excluded: chain Z residue 323 LEU Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 473 THR Chi-restraints excluded: chain Z residue 475 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 320 optimal weight: 40.0000 chunk 313 optimal weight: 20.0000 chunk 169 optimal weight: 40.0000 chunk 391 optimal weight: 9.9990 chunk 502 optimal weight: 20.0000 chunk 695 optimal weight: 5.9990 chunk 428 optimal weight: 0.5980 chunk 459 optimal weight: 20.0000 chunk 432 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 211 optimal weight: 50.0000 overall best weight: 9.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 GLN ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 820 HIS C 821 HIS C1147 ASN ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 820 HIS E 821 HIS ** E 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS F 821 HIS ** F 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 403 GLN ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 820 HIS G 821 HIS G1074 GLN ** G1102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 195 HIS q 90 ASN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 320 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.190437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.174787 restraints weight = 278363.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.173942 restraints weight = 310031.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.174584 restraints weight = 243435.697| |-----------------------------------------------------------------------------| r_work (final): 0.4537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5384 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 58361 Z= 0.222 Angle : 0.657 14.309 79551 Z= 0.329 Chirality : 0.044 0.355 9141 Planarity : 0.005 0.059 10399 Dihedral : 4.688 26.862 8089 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.26 % Allowed : 8.09 % Favored : 91.65 % Rotamer: Outliers : 3.29 % Allowed : 15.83 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.10), residues: 7304 helix: 0.24 (0.11), residues: 2393 sheet: -1.08 (0.16), residues: 1007 loop : -1.63 (0.10), residues: 3904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 276 HIS 0.013 0.001 HIS G1064 PHE 0.045 0.002 PHE h 546 TYR 0.019 0.002 TYR F 644 ARG 0.008 0.001 ARG R 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 701 time to evaluate : 4.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.4386 (mmp) cc_final: 0.3912 (mmt) REVERT: A 530 MET cc_start: -0.0381 (ppp) cc_final: -0.1022 (ppp) REVERT: A 686 MET cc_start: 0.5557 (pmm) cc_final: 0.5036 (pmm) REVERT: A 917 MET cc_start: 0.1094 (ttm) cc_final: 0.0843 (ttm) REVERT: A 920 MET cc_start: 0.0788 (ttp) cc_final: -0.0125 (tmm) REVERT: A 958 MET cc_start: 0.4685 (mmp) cc_final: 0.3536 (mtp) REVERT: A 1150 PHE cc_start: 0.4616 (m-80) cc_final: 0.4292 (t80) REVERT: C 115 MET cc_start: 0.7124 (pmm) cc_final: 0.6415 (ptm) REVERT: C 196 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8162 (tt) REVERT: C 431 MET cc_start: 0.5867 (mmt) cc_final: 0.5612 (mmt) REVERT: C 520 MET cc_start: 0.3744 (ptt) cc_final: 0.3501 (ptt) REVERT: C 789 MET cc_start: 0.2056 (mmm) cc_final: 0.1846 (mmt) REVERT: C 958 MET cc_start: 0.4370 (mmt) cc_final: 0.4088 (mtm) REVERT: C 1004 LYS cc_start: 0.5172 (mmtm) cc_final: 0.3343 (mttt) REVERT: C 1189 ARG cc_start: 0.3679 (mmt180) cc_final: 0.2799 (mtm180) REVERT: E 431 MET cc_start: 0.6198 (OUTLIER) cc_final: 0.5193 (mmt) REVERT: E 520 MET cc_start: 0.3807 (ptt) cc_final: 0.3291 (ptt) REVERT: E 530 MET cc_start: 0.0522 (ptm) cc_final: -0.0148 (ppp) REVERT: E 1157 MET cc_start: 0.0623 (mtt) cc_final: -0.1430 (tpp) REVERT: E 1189 ARG cc_start: 0.3662 (mmt180) cc_final: 0.2794 (mtm180) REVERT: F 421 MET cc_start: 0.5899 (mmt) cc_final: 0.5449 (mmt) REVERT: F 423 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7531 (tpp) REVERT: F 530 MET cc_start: 0.0659 (ppp) cc_final: 0.0233 (ppp) REVERT: F 1157 MET cc_start: 0.0717 (mtt) cc_final: -0.1212 (tpp) REVERT: F 1189 ARG cc_start: 0.4183 (mmt-90) cc_final: 0.3065 (mtm180) REVERT: G 87 LEU cc_start: 0.7860 (tp) cc_final: 0.7554 (tt) REVERT: G 115 MET cc_start: 0.7183 (pmm) cc_final: 0.6825 (ptm) REVERT: G 306 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7771 (tt) REVERT: G 686 MET cc_start: 0.5622 (OUTLIER) cc_final: 0.5077 (ptp) REVERT: G 1157 MET cc_start: -0.0153 (mtt) cc_final: -0.2191 (tpp) REVERT: G 1189 ARG cc_start: 0.4391 (mmt180) cc_final: 0.3905 (mmp-170) REVERT: G 1376 HIS cc_start: 0.3892 (t-90) cc_final: 0.3584 (t-170) REVERT: h 1 MET cc_start: 0.4985 (ttm) cc_final: 0.4448 (ttp) REVERT: h 511 ASP cc_start: 0.5343 (t70) cc_final: 0.5110 (t70) REVERT: h 539 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6630 (pm20) REVERT: h 546 PHE cc_start: 0.5967 (p90) cc_final: 0.5624 (p90) REVERT: R 70 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7538 (ttp80) REVERT: V 192 HIS cc_start: 0.6625 (t70) cc_final: 0.6416 (t-90) REVERT: Z 219 ARG cc_start: 0.8060 (tpp80) cc_final: 0.7795 (tpp80) outliers start: 198 outliers final: 146 residues processed: 811 average time/residue: 0.5349 time to fit residues: 741.7296 Evaluate side-chains 818 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 665 time to evaluate : 4.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 996 THR Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1099 VAL Chi-restraints excluded: chain A residue 1100 HIS Chi-restraints excluded: chain A residue 1207 VAL Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1217 TYR Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 306 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 997 ASN Chi-restraints excluded: chain C residue 1036 PHE Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1099 VAL Chi-restraints excluded: chain C residue 1207 VAL Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain C residue 1217 TYR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 423 MET Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 622 MET Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1207 VAL Chi-restraints excluded: chain E residue 1216 GLN Chi-restraints excluded: chain E residue 1217 TYR Chi-restraints excluded: chain E residue 1362 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 246 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 380 VAL Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 423 MET Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 792 HIS Chi-restraints excluded: chain F residue 864 VAL Chi-restraints excluded: chain F residue 944 ASN Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 996 THR Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1082 LEU Chi-restraints excluded: chain F residue 1099 VAL Chi-restraints excluded: chain F residue 1207 VAL Chi-restraints excluded: chain F residue 1209 MET Chi-restraints excluded: chain F residue 1217 TYR Chi-restraints excluded: chain F residue 1362 LEU Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 423 MET Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 686 MET Chi-restraints excluded: chain G residue 743 LEU Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 997 ASN Chi-restraints excluded: chain G residue 1071 VAL Chi-restraints excluded: chain G residue 1209 MET Chi-restraints excluded: chain G residue 1215 LEU Chi-restraints excluded: chain G residue 1217 TYR Chi-restraints excluded: chain G residue 1375 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 168 MET Chi-restraints excluded: chain h residue 476 VAL Chi-restraints excluded: chain h residue 539 GLU Chi-restraints excluded: chain h residue 610 MET Chi-restraints excluded: chain u residue 55 LEU Chi-restraints excluded: chain u residue 71 MET Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 70 ARG Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 149 ILE Chi-restraints excluded: chain V residue 283 LEU Chi-restraints excluded: chain V residue 302 SER Chi-restraints excluded: chain V residue 310 THR Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 224 SER Chi-restraints excluded: chain Z residue 226 TYR Chi-restraints excluded: chain Z residue 238 PHE Chi-restraints excluded: chain Z residue 263 LEU Chi-restraints excluded: chain Z residue 272 CYS Chi-restraints excluded: chain Z residue 298 ASN Chi-restraints excluded: chain Z residue 305 TRP Chi-restraints excluded: chain Z residue 321 VAL Chi-restraints excluded: chain Z residue 323 LEU Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 444 VAL Chi-restraints excluded: chain Z residue 473 THR Chi-restraints excluded: chain Z residue 475 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 710 optimal weight: 0.4980 chunk 626 optimal weight: 8.9990 chunk 153 optimal weight: 0.8980 chunk 334 optimal weight: 40.0000 chunk 254 optimal weight: 9.9990 chunk 145 optimal weight: 2.9990 chunk 301 optimal weight: 50.0000 chunk 24 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 40 optimal weight: 50.0000 chunk 12 optimal weight: 20.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 ASN ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 820 HIS ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN ** E 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 820 HIS ** E 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS ** F 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 820 HIS ** G1102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1216 GLN h 558 HIS q 90 ASN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 GLN Z 320 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4790 r_free = 0.4790 target = 0.193924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.182899 restraints weight = 183551.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.175245 restraints weight = 202252.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.175526 restraints weight = 194050.799| |-----------------------------------------------------------------------------| r_work (final): 0.4597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5318 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 58361 Z= 0.169 Angle : 0.635 16.181 79551 Z= 0.310 Chirality : 0.043 0.302 9141 Planarity : 0.005 0.054 10399 Dihedral : 4.493 26.163 8089 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.38 % Favored : 92.42 % Rotamer: Outliers : 2.87 % Allowed : 17.24 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.10), residues: 7304 helix: 0.36 (0.11), residues: 2390 sheet: -1.05 (0.16), residues: 994 loop : -1.54 (0.10), residues: 3920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 305 HIS 0.013 0.001 HIS C1064 PHE 0.042 0.001 PHE C 523 TYR 0.019 0.001 TYR V 184 ARG 0.006 0.000 ARG R 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 713 time to evaluate : 5.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.4934 (mmp) cc_final: 0.4245 (mmt) REVERT: A 530 MET cc_start: 0.0080 (ppp) cc_final: -0.0547 (ppp) REVERT: A 686 MET cc_start: 0.5444 (pmm) cc_final: 0.4901 (pmm) REVERT: A 920 MET cc_start: 0.0070 (ttp) cc_final: -0.0803 (tmm) REVERT: A 958 MET cc_start: 0.4559 (mmp) cc_final: 0.2999 (mtp) REVERT: A 1150 PHE cc_start: 0.4080 (m-80) cc_final: 0.3847 (t80) REVERT: A 1219 ARG cc_start: 0.7100 (mtt-85) cc_final: 0.6792 (mmt90) REVERT: C 115 MET cc_start: 0.6909 (pmm) cc_final: 0.6419 (ptm) REVERT: C 196 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8185 (tt) REVERT: C 431 MET cc_start: 0.6505 (mmt) cc_final: 0.6135 (mmt) REVERT: C 530 MET cc_start: 0.2199 (ppp) cc_final: 0.1993 (ppp) REVERT: C 726 ILE cc_start: 0.2454 (mp) cc_final: 0.2137 (mm) REVERT: C 789 MET cc_start: 0.2219 (mmm) cc_final: 0.1975 (mmt) REVERT: C 958 MET cc_start: 0.3591 (mmt) cc_final: 0.3077 (ptm) REVERT: C 1004 LYS cc_start: 0.4922 (mmtm) cc_final: 0.3496 (mttt) REVERT: C 1157 MET cc_start: 0.0251 (mtt) cc_final: -0.1615 (tpp) REVERT: C 1189 ARG cc_start: 0.3616 (mmt180) cc_final: 0.2717 (mtm180) REVERT: E 431 MET cc_start: 0.6316 (OUTLIER) cc_final: 0.5922 (mpp) REVERT: E 530 MET cc_start: 0.1120 (ptm) cc_final: 0.0118 (ppp) REVERT: E 686 MET cc_start: 0.5904 (OUTLIER) cc_final: 0.5430 (pmm) REVERT: E 1157 MET cc_start: -0.0124 (mtt) cc_final: -0.1794 (tpp) REVERT: E 1189 ARG cc_start: 0.3408 (mmt180) cc_final: 0.2484 (mtm180) REVERT: F 421 MET cc_start: 0.6086 (mmt) cc_final: 0.5584 (mmt) REVERT: F 431 MET cc_start: 0.5815 (mmp) cc_final: 0.5575 (mmt) REVERT: F 522 ARG cc_start: 0.4402 (OUTLIER) cc_final: 0.3987 (ptt90) REVERT: F 530 MET cc_start: 0.1608 (ppp) cc_final: 0.1362 (ppp) REVERT: F 645 MET cc_start: 0.3438 (mpp) cc_final: 0.3040 (ptp) REVERT: F 1157 MET cc_start: 0.0493 (mtt) cc_final: -0.1326 (tpp) REVERT: F 1189 ARG cc_start: 0.4235 (mmt-90) cc_final: 0.3207 (mtm180) REVERT: G 531 MET cc_start: -0.3230 (mmp) cc_final: -0.3502 (mmp) REVERT: G 686 MET cc_start: 0.6135 (OUTLIER) cc_final: 0.5756 (ptp) REVERT: G 860 GLN cc_start: 0.0199 (OUTLIER) cc_final: -0.0332 (mm-40) REVERT: G 1157 MET cc_start: -0.0449 (mtt) cc_final: -0.2247 (tpp) REVERT: G 1189 ARG cc_start: 0.3926 (mmt180) cc_final: 0.3422 (mmp-170) REVERT: G 1376 HIS cc_start: 0.3658 (t-90) cc_final: 0.3399 (t70) REVERT: h 124 TYR cc_start: 0.5770 (m-80) cc_final: 0.5509 (m-80) REVERT: h 169 ARG cc_start: 0.6242 (ptp90) cc_final: 0.4193 (mtm110) REVERT: h 173 HIS cc_start: 0.4663 (m90) cc_final: 0.3457 (m90) REVERT: h 641 LEU cc_start: 0.6269 (mt) cc_final: 0.6057 (mt) REVERT: R 70 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7598 (ttp80) REVERT: V 152 LYS cc_start: 0.8417 (mtpt) cc_final: 0.7915 (tttt) REVERT: V 192 HIS cc_start: 0.6393 (t70) cc_final: 0.6166 (t70) REVERT: Z 219 ARG cc_start: 0.8512 (tpp80) cc_final: 0.7935 (tpp80) outliers start: 173 outliers final: 124 residues processed: 801 average time/residue: 0.5378 time to fit residues: 730.0771 Evaluate side-chains 805 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 674 time to evaluate : 4.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1217 TYR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 997 ASN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1169 ILE Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain C residue 1354 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 423 MET Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 686 MET Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 1072 VAL Chi-restraints excluded: chain E residue 1082 LEU Chi-restraints excluded: chain E residue 1207 VAL Chi-restraints excluded: chain E residue 1216 GLN Chi-restraints excluded: chain E residue 1217 TYR Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 201 LEU Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 258 TYR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 383 ASP Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 522 ARG Chi-restraints excluded: chain F residue 792 HIS Chi-restraints excluded: chain F residue 864 VAL Chi-restraints excluded: chain F residue 944 ASN Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 996 THR Chi-restraints excluded: chain F residue 1064 HIS Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1082 LEU Chi-restraints excluded: chain F residue 1209 MET Chi-restraints excluded: chain F residue 1217 TYR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 423 MET Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 686 MET Chi-restraints excluded: chain G residue 691 THR Chi-restraints excluded: chain G residue 860 GLN Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 996 THR Chi-restraints excluded: chain G residue 997 ASN Chi-restraints excluded: chain G residue 1071 VAL Chi-restraints excluded: chain G residue 1209 MET Chi-restraints excluded: chain G residue 1215 LEU Chi-restraints excluded: chain G residue 1217 TYR Chi-restraints excluded: chain G residue 1375 VAL Chi-restraints excluded: chain h residue 13 LEU Chi-restraints excluded: chain h residue 476 VAL Chi-restraints excluded: chain u residue 55 LEU Chi-restraints excluded: chain u residue 71 MET Chi-restraints excluded: chain y residue 3136 MET Chi-restraints excluded: chain R residue 11 LEU Chi-restraints excluded: chain R residue 70 ARG Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 283 LEU Chi-restraints excluded: chain V residue 302 SER Chi-restraints excluded: chain V residue 310 THR Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 238 PHE Chi-restraints excluded: chain Z residue 272 CYS Chi-restraints excluded: chain Z residue 283 GLU Chi-restraints excluded: chain Z residue 298 ASN Chi-restraints excluded: chain Z residue 305 TRP Chi-restraints excluded: chain Z residue 321 VAL Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 473 THR Chi-restraints excluded: chain Z residue 475 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 458 optimal weight: 4.9990 chunk 696 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 713 optimal weight: 6.9990 chunk 607 optimal weight: 0.5980 chunk 343 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 500 optimal weight: 40.0000 chunk 392 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 820 HIS ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 GLN E 820 HIS E 860 GLN ** E 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 248 HIS ** F 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS ** F 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 820 HIS ** G 882 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 320 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4807 r_free = 0.4807 target = 0.192623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.176778 restraints weight = 276102.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.176188 restraints weight = 290588.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.176728 restraints weight = 219499.856| |-----------------------------------------------------------------------------| r_work (final): 0.4566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5295 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 58361 Z= 0.160 Angle : 0.633 16.755 79551 Z= 0.307 Chirality : 0.043 0.290 9141 Planarity : 0.004 0.053 10399 Dihedral : 4.327 25.478 8089 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.60 % Favored : 92.20 % Rotamer: Outliers : 2.59 % Allowed : 18.02 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.10), residues: 7304 helix: 0.57 (0.11), residues: 2359 sheet: -1.06 (0.17), residues: 932 loop : -1.45 (0.10), residues: 4013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 276 HIS 0.013 0.001 HIS C1064 PHE 0.025 0.001 PHE A1077 TYR 0.017 0.001 TYR R 52 ARG 0.006 0.000 ARG h 536 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 728 time to evaluate : 4.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.4614 (mmp) cc_final: 0.4071 (mmt) REVERT: A 520 MET cc_start: 0.5398 (ppp) cc_final: 0.4927 (ppp) REVERT: A 530 MET cc_start: -0.0629 (ppp) cc_final: -0.1123 (ppp) REVERT: A 686 MET cc_start: 0.5215 (pmm) cc_final: 0.4744 (pmm) REVERT: A 920 MET cc_start: 0.0586 (ttp) cc_final: -0.0617 (tmm) REVERT: A 958 MET cc_start: 0.4525 (mmp) cc_final: 0.3624 (mtp) REVERT: A 1150 PHE cc_start: 0.4022 (m-80) cc_final: 0.3752 (t80) REVERT: C 115 MET cc_start: 0.6862 (pmm) cc_final: 0.6071 (ptm) REVERT: C 196 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8442 (tt) REVERT: C 431 MET cc_start: 0.5838 (mmt) cc_final: 0.5579 (mmt) REVERT: C 726 ILE cc_start: 0.2185 (mp) cc_final: 0.1916 (mm) REVERT: C 917 MET cc_start: 0.1802 (ttm) cc_final: 0.1439 (ttp) REVERT: C 958 MET cc_start: 0.4112 (mmt) cc_final: 0.3801 (ptm) REVERT: C 1004 LYS cc_start: 0.5038 (mmtm) cc_final: 0.3270 (mttt) REVERT: C 1157 MET cc_start: -0.0068 (mtt) cc_final: -0.1700 (tpp) REVERT: C 1189 ARG cc_start: 0.3733 (mmt180) cc_final: 0.2860 (mtm180) REVERT: E 530 MET cc_start: 0.1065 (ptm) cc_final: 0.0165 (ppp) REVERT: E 686 MET cc_start: 0.5786 (OUTLIER) cc_final: 0.5474 (pmm) REVERT: E 789 MET cc_start: -0.0102 (OUTLIER) cc_final: -0.0494 (mmt) REVERT: E 1157 MET cc_start: 0.0037 (mtt) cc_final: -0.1503 (tpp) REVERT: E 1189 ARG cc_start: 0.3661 (mmt180) cc_final: 0.2573 (mtm180) REVERT: E 1361 MET cc_start: 0.4950 (mpp) cc_final: 0.4179 (mpp) REVERT: F 522 ARG cc_start: 0.4005 (OUTLIER) cc_final: 0.3577 (ptt90) REVERT: F 645 MET cc_start: 0.4235 (mpp) cc_final: 0.3297 (ptp) REVERT: F 1157 MET cc_start: 0.0262 (mtt) cc_final: -0.1122 (tpp) REVERT: F 1189 ARG cc_start: 0.4683 (mmt-90) cc_final: 0.3554 (mtm180) REVERT: G 421 MET cc_start: 0.6057 (tpp) cc_final: 0.5848 (tpt) REVERT: G 531 MET cc_start: -0.3699 (mmp) cc_final: -0.3932 (mmp) REVERT: G 686 MET cc_start: 0.5790 (OUTLIER) cc_final: 0.5187 (ptp) REVERT: G 860 GLN cc_start: 0.2005 (OUTLIER) cc_final: 0.0689 (mm-40) REVERT: G 1157 MET cc_start: -0.0333 (mtt) cc_final: -0.1764 (tpp) REVERT: G 1189 ARG cc_start: 0.4204 (mmt180) cc_final: 0.3681 (mmp-170) REVERT: G 1376 HIS cc_start: 0.3259 (t-90) cc_final: 0.3058 (t70) REVERT: h 124 TYR cc_start: 0.5845 (m-80) cc_final: 0.5425 (m-80) REVERT: h 168 MET cc_start: 0.5573 (mmp) cc_final: 0.5324 (mmp) REVERT: h 389 HIS cc_start: 0.6352 (m170) cc_final: 0.6039 (m90) REVERT: R 70 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7470 (ttp80) REVERT: V 152 LYS cc_start: 0.8369 (mtpt) cc_final: 0.7744 (ttpt) REVERT: V 190 LEU cc_start: 0.7146 (mt) cc_final: 0.6705 (mt) REVERT: Z 219 ARG cc_start: 0.7991 (tpp80) cc_final: 0.7438 (tpp80) REVERT: Z 450 MET cc_start: 0.7303 (tpp) cc_final: 0.6705 (tpp) outliers start: 156 outliers final: 107 residues processed: 808 average time/residue: 0.5454 time to fit residues: 750.7173 Evaluate side-chains 791 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 677 time to evaluate : 4.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 258 TYR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1217 TYR Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 997 ASN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1169 ILE Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 686 MET Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 1072 VAL Chi-restraints excluded: chain E residue 1082 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 258 TYR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 522 ARG Chi-restraints excluded: chain F residue 864 VAL Chi-restraints excluded: chain F residue 944 ASN Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 996 THR Chi-restraints excluded: chain F residue 1064 HIS Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1209 MET Chi-restraints excluded: chain F residue 1217 TYR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 423 MET Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 686 MET Chi-restraints excluded: chain G residue 691 THR Chi-restraints excluded: chain G residue 860 GLN Chi-restraints excluded: chain G residue 917 MET Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 996 THR Chi-restraints excluded: chain G residue 997 ASN Chi-restraints excluded: chain G residue 1071 VAL Chi-restraints excluded: chain G residue 1217 TYR Chi-restraints excluded: chain G residue 1356 SER Chi-restraints excluded: chain G residue 1375 VAL Chi-restraints excluded: chain h residue 476 VAL Chi-restraints excluded: chain u residue 13 TRP Chi-restraints excluded: chain u residue 55 LEU Chi-restraints excluded: chain u residue 71 MET Chi-restraints excluded: chain y residue 3136 MET Chi-restraints excluded: chain R residue 70 ARG Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 46 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 238 PHE Chi-restraints excluded: chain Z residue 272 CYS Chi-restraints excluded: chain Z residue 283 GLU Chi-restraints excluded: chain Z residue 318 LEU Chi-restraints excluded: chain Z residue 321 VAL Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 473 THR Chi-restraints excluded: chain Z residue 475 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 66 optimal weight: 20.0000 chunk 458 optimal weight: 4.9990 chunk 693 optimal weight: 6.9990 chunk 250 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 689 optimal weight: 10.0000 chunk 283 optimal weight: 10.0000 chunk 712 optimal weight: 5.9990 chunk 657 optimal weight: 8.9990 chunk 673 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 820 HIS ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 793 ASN E 820 HIS ** E 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS ** F 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 820 HIS ** G 882 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 320 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.190814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.169494 restraints weight = 225706.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.169847 restraints weight = 189530.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.169819 restraints weight = 167330.729| |-----------------------------------------------------------------------------| r_work (final): 0.4504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5617 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 58361 Z= 0.183 Angle : 0.648 17.278 79551 Z= 0.316 Chirality : 0.043 0.332 9141 Planarity : 0.005 0.052 10399 Dihedral : 4.410 30.628 8089 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.93 % Favored : 91.89 % Rotamer: Outliers : 2.48 % Allowed : 18.42 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.10), residues: 7304 helix: 0.48 (0.11), residues: 2385 sheet: -0.96 (0.16), residues: 998 loop : -1.48 (0.10), residues: 3921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 276 HIS 0.016 0.001 HIS G1064 PHE 0.060 0.002 PHE F 244 TYR 0.023 0.001 TYR V 184 ARG 0.007 0.000 ARG F1135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 700 time to evaluate : 4.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 3136 MET cc_start: 0.6365 (tpp) cc_final: 0.5425 (tmm) REVERT: A 431 MET cc_start: 0.4620 (mmp) cc_final: 0.4011 (mmt) REVERT: A 520 MET cc_start: 0.3599 (ppp) cc_final: 0.3348 (ppp) REVERT: A 530 MET cc_start: 0.0262 (ppp) cc_final: -0.0407 (ppp) REVERT: A 645 MET cc_start: 0.4568 (mpp) cc_final: 0.4328 (mpp) REVERT: A 920 MET cc_start: -0.0398 (ttp) cc_final: -0.1459 (tmm) REVERT: A 958 MET cc_start: 0.4609 (mmp) cc_final: 0.3013 (mtm) REVERT: A 1150 PHE cc_start: 0.3906 (m-80) cc_final: 0.3703 (t80) REVERT: C 25 ILE cc_start: 0.2488 (OUTLIER) cc_final: 0.1841 (pp) REVERT: C 115 MET cc_start: 0.6854 (pmm) cc_final: 0.6128 (ptm) REVERT: C 196 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.8096 (tt) REVERT: C 431 MET cc_start: 0.6423 (mmt) cc_final: 0.6064 (mmt) REVERT: C 726 ILE cc_start: 0.3444 (mp) cc_final: 0.3074 (mm) REVERT: C 958 MET cc_start: 0.3548 (mmt) cc_final: 0.2789 (mtm) REVERT: C 1004 LYS cc_start: 0.4683 (mmtm) cc_final: 0.3541 (mttt) REVERT: C 1157 MET cc_start: 0.0239 (mtt) cc_final: -0.1693 (tpp) REVERT: C 1189 ARG cc_start: 0.3637 (mmt180) cc_final: 0.2762 (mtm180) REVERT: E 530 MET cc_start: 0.1179 (ptm) cc_final: 0.0261 (ppp) REVERT: E 686 MET cc_start: 0.5916 (OUTLIER) cc_final: 0.5435 (pmm) REVERT: E 789 MET cc_start: -0.0918 (OUTLIER) cc_final: -0.1124 (mmt) REVERT: E 1157 MET cc_start: -0.0425 (mtt) cc_final: -0.1979 (tpp) REVERT: E 1189 ARG cc_start: 0.3517 (mmt180) cc_final: 0.2578 (mtm180) REVERT: F 522 ARG cc_start: 0.4563 (OUTLIER) cc_final: 0.4091 (ptt90) REVERT: F 530 MET cc_start: 0.1622 (ppp) cc_final: 0.0957 (ppp) REVERT: F 1157 MET cc_start: 0.0422 (mtt) cc_final: -0.1331 (tpp) REVERT: F 1189 ARG cc_start: 0.4846 (mmt-90) cc_final: 0.3711 (mtm180) REVERT: G 475 MET cc_start: 0.6890 (tpp) cc_final: 0.6441 (tpp) REVERT: G 530 MET cc_start: 0.1195 (ppp) cc_final: 0.0603 (ppp) REVERT: G 686 MET cc_start: 0.6261 (OUTLIER) cc_final: 0.5987 (ptp) REVERT: G 860 GLN cc_start: 0.0174 (OUTLIER) cc_final: -0.0293 (mm-40) REVERT: G 1157 MET cc_start: -0.0551 (mtt) cc_final: -0.2302 (tpp) REVERT: G 1189 ARG cc_start: 0.3788 (mmt180) cc_final: 0.3362 (mmp-170) REVERT: G 1376 HIS cc_start: 0.3770 (t-90) cc_final: 0.3536 (t70) REVERT: h 124 TYR cc_start: 0.5914 (m-80) cc_final: 0.5538 (m-80) REVERT: h 539 GLU cc_start: 0.6679 (pm20) cc_final: 0.6250 (pm20) REVERT: R 70 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8067 (ttp80) REVERT: V 190 LEU cc_start: 0.7293 (mt) cc_final: 0.6985 (mm) REVERT: V 314 GLN cc_start: 0.8367 (pm20) cc_final: 0.7987 (pm20) REVERT: Z 219 ARG cc_start: 0.8404 (tpp80) cc_final: 0.7721 (tpp80) REVERT: Z 450 MET cc_start: 0.7450 (tpp) cc_final: 0.6814 (tpp) outliers start: 149 outliers final: 124 residues processed: 781 average time/residue: 0.5248 time to fit residues: 703.5693 Evaluate side-chains 795 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 663 time to evaluate : 4.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 997 ASN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1112 LEU Chi-restraints excluded: chain C residue 1169 ILE Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain C residue 1217 TYR Chi-restraints excluded: chain C residue 1354 LEU Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 686 MET Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 1072 VAL Chi-restraints excluded: chain E residue 1207 VAL Chi-restraints excluded: chain E residue 1209 MET Chi-restraints excluded: chain E residue 1216 GLN Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 522 ARG Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 864 VAL Chi-restraints excluded: chain F residue 944 ASN Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 996 THR Chi-restraints excluded: chain F residue 1064 HIS Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1099 VAL Chi-restraints excluded: chain F residue 1209 MET Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 686 MET Chi-restraints excluded: chain G residue 691 THR Chi-restraints excluded: chain G residue 860 GLN Chi-restraints excluded: chain G residue 917 MET Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 996 THR Chi-restraints excluded: chain G residue 997 ASN Chi-restraints excluded: chain G residue 1071 VAL Chi-restraints excluded: chain G residue 1215 LEU Chi-restraints excluded: chain G residue 1217 TYR Chi-restraints excluded: chain G residue 1356 SER Chi-restraints excluded: chain G residue 1375 VAL Chi-restraints excluded: chain h residue 476 VAL Chi-restraints excluded: chain u residue 13 TRP Chi-restraints excluded: chain u residue 55 LEU Chi-restraints excluded: chain u residue 71 MET Chi-restraints excluded: chain R residue 70 ARG Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 295 VAL Chi-restraints excluded: chain V residue 304 VAL Chi-restraints excluded: chain V residue 310 THR Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 238 PHE Chi-restraints excluded: chain Z residue 272 CYS Chi-restraints excluded: chain Z residue 318 LEU Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 473 THR Chi-restraints excluded: chain Z residue 475 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 115 optimal weight: 10.0000 chunk 13 optimal weight: 30.0000 chunk 269 optimal weight: 0.0470 chunk 661 optimal weight: 10.0000 chunk 532 optimal weight: 40.0000 chunk 471 optimal weight: 20.0000 chunk 17 optimal weight: 30.0000 chunk 457 optimal weight: 40.0000 chunk 308 optimal weight: 20.0000 chunk 419 optimal weight: 50.0000 chunk 309 optimal weight: 6.9990 overall best weight: 9.4092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN A 129 HIS ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 820 HIS ** C1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 820 HIS ** E 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 108 GLN ** F 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 653 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS ** F 895 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 820 HIS ** G 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1143 ASN ** G1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 237 GLN h 389 HIS h 446 GLN q 90 ASN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 314 GLN Z 320 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.188613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.172367 restraints weight = 278178.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.171390 restraints weight = 342316.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.171878 restraints weight = 247456.542| |-----------------------------------------------------------------------------| r_work (final): 0.4499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5547 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 58361 Z= 0.229 Angle : 0.701 17.853 79551 Z= 0.345 Chirality : 0.045 0.327 9141 Planarity : 0.005 0.056 10399 Dihedral : 4.731 29.228 8089 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.34 % Favored : 91.47 % Rotamer: Outliers : 2.59 % Allowed : 18.95 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.10), residues: 7304 helix: 0.23 (0.11), residues: 2396 sheet: -1.08 (0.16), residues: 961 loop : -1.55 (0.10), residues: 3947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 276 HIS 0.018 0.001 HIS E1064 PHE 0.059 0.002 PHE F 244 TYR 0.014 0.002 TYR C 409 ARG 0.010 0.001 ARG V 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14608 Ramachandran restraints generated. 7304 Oldfield, 0 Emsley, 7304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 690 time to evaluate : 5.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 431 MET cc_start: 0.4137 (mmp) cc_final: 0.3451 (mmt) REVERT: A 520 MET cc_start: 0.4717 (ppp) cc_final: 0.4460 (ppp) REVERT: A 530 MET cc_start: -0.0270 (ppp) cc_final: -0.0873 (ppp) REVERT: A 748 PHE cc_start: 0.1457 (t80) cc_final: 0.1091 (t80) REVERT: A 920 MET cc_start: 0.0670 (ttp) cc_final: -0.0588 (tmm) REVERT: A 958 MET cc_start: 0.4681 (mmp) cc_final: 0.3843 (mtm) REVERT: A 1150 PHE cc_start: 0.4010 (m-80) cc_final: 0.3772 (t80) REVERT: C 25 ILE cc_start: 0.1343 (OUTLIER) cc_final: 0.0963 (pt) REVERT: C 115 MET cc_start: 0.7118 (pmm) cc_final: 0.6312 (ptm) REVERT: C 196 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8329 (tt) REVERT: C 245 MET cc_start: 0.7361 (mmm) cc_final: 0.6950 (mmm) REVERT: C 726 ILE cc_start: 0.2614 (mp) cc_final: 0.2092 (mm) REVERT: C 1004 LYS cc_start: 0.5202 (mmtm) cc_final: 0.3342 (mttt) REVERT: C 1108 VAL cc_start: 0.7819 (t) cc_final: 0.7609 (m) REVERT: C 1189 ARG cc_start: 0.4434 (mmt180) cc_final: 0.3508 (mtm180) REVERT: E 530 MET cc_start: 0.1252 (ptm) cc_final: 0.0207 (ppp) REVERT: E 686 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5432 (pmm) REVERT: E 789 MET cc_start: -0.0041 (OUTLIER) cc_final: -0.0473 (mmt) REVERT: E 945 MET cc_start: 0.4410 (ttt) cc_final: 0.3882 (ttm) REVERT: E 1157 MET cc_start: -0.0153 (mtt) cc_final: -0.1888 (tpp) REVERT: E 1189 ARG cc_start: 0.3703 (mmt180) cc_final: 0.2886 (mtm180) REVERT: F 945 MET cc_start: 0.2377 (ttt) cc_final: 0.1668 (tmm) REVERT: F 1157 MET cc_start: 0.0862 (mtt) cc_final: -0.1025 (tpp) REVERT: F 1189 ARG cc_start: 0.5132 (mmt-90) cc_final: 0.3800 (mtm180) REVERT: G 860 GLN cc_start: 0.1552 (OUTLIER) cc_final: 0.0233 (mm-40) REVERT: G 1157 MET cc_start: 0.0002 (mtt) cc_final: -0.2158 (tpp) REVERT: G 1189 ARG cc_start: 0.4393 (mmt180) cc_final: 0.3869 (mmp-170) REVERT: G 1376 HIS cc_start: 0.3859 (t-90) cc_final: 0.3487 (t70) REVERT: h 124 TYR cc_start: 0.5941 (m-80) cc_final: 0.5499 (m-80) REVERT: h 168 MET cc_start: 0.5551 (mmp) cc_final: 0.5331 (mmp) REVERT: R 4 MET cc_start: 0.7234 (mpp) cc_final: 0.6918 (mmt) REVERT: R 70 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7544 (tmm160) REVERT: R 270 TYR cc_start: 0.4915 (t80) cc_final: 0.4648 (t80) REVERT: V 152 LYS cc_start: 0.8399 (ttpt) cc_final: 0.8160 (ttpt) REVERT: V 190 LEU cc_start: 0.7334 (mt) cc_final: 0.6889 (mm) REVERT: V 192 HIS cc_start: 0.6315 (t70) cc_final: 0.6100 (t70) REVERT: V 208 MET cc_start: 0.7490 (ppp) cc_final: 0.6298 (ttm) REVERT: V 276 TRP cc_start: 0.5377 (m100) cc_final: 0.4876 (m100) REVERT: V 290 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7026 (ttm-80) REVERT: Z 174 GLN cc_start: 0.7728 (pt0) cc_final: 0.7066 (tm-30) REVERT: Z 450 MET cc_start: 0.7438 (tpp) cc_final: 0.6794 (tpp) outliers start: 156 outliers final: 127 residues processed: 779 average time/residue: 0.5334 time to fit residues: 710.2024 Evaluate side-chains 791 residues out of total 6198 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 657 time to evaluate : 4.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 194 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 557 PHE Chi-restraints excluded: chain A residue 864 VAL Chi-restraints excluded: chain A residue 876 THR Chi-restraints excluded: chain A residue 979 VAL Chi-restraints excluded: chain A residue 1072 VAL Chi-restraints excluded: chain A residue 1213 THR Chi-restraints excluded: chain A residue 1215 LEU Chi-restraints excluded: chain A residue 1375 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 194 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 200 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 743 LEU Chi-restraints excluded: chain C residue 876 THR Chi-restraints excluded: chain C residue 959 MET Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 996 THR Chi-restraints excluded: chain C residue 997 ASN Chi-restraints excluded: chain C residue 1072 VAL Chi-restraints excluded: chain C residue 1112 LEU Chi-restraints excluded: chain C residue 1169 ILE Chi-restraints excluded: chain C residue 1209 MET Chi-restraints excluded: chain C residue 1217 TYR Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 115 MET Chi-restraints excluded: chain E residue 140 SER Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain E residue 234 LEU Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain E residue 306 ILE Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 557 PHE Chi-restraints excluded: chain E residue 686 MET Chi-restraints excluded: chain E residue 789 MET Chi-restraints excluded: chain E residue 979 VAL Chi-restraints excluded: chain E residue 996 THR Chi-restraints excluded: chain E residue 1072 VAL Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1112 LEU Chi-restraints excluded: chain E residue 1209 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 194 ASP Chi-restraints excluded: chain F residue 213 ILE Chi-restraints excluded: chain F residue 234 LEU Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 263 VAL Chi-restraints excluded: chain F residue 275 ILE Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 407 VAL Chi-restraints excluded: chain F residue 498 LEU Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain F residue 850 VAL Chi-restraints excluded: chain F residue 864 VAL Chi-restraints excluded: chain F residue 944 ASN Chi-restraints excluded: chain F residue 979 VAL Chi-restraints excluded: chain F residue 996 THR Chi-restraints excluded: chain F residue 1064 HIS Chi-restraints excluded: chain F residue 1072 VAL Chi-restraints excluded: chain F residue 1082 LEU Chi-restraints excluded: chain F residue 1099 VAL Chi-restraints excluded: chain F residue 1209 MET Chi-restraints excluded: chain F residue 1219 ARG Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 140 SER Chi-restraints excluded: chain G residue 200 LEU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 275 ILE Chi-restraints excluded: chain G residue 380 VAL Chi-restraints excluded: chain G residue 384 LEU Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 498 LEU Chi-restraints excluded: chain G residue 860 GLN Chi-restraints excluded: chain G residue 917 MET Chi-restraints excluded: chain G residue 979 VAL Chi-restraints excluded: chain G residue 996 THR Chi-restraints excluded: chain G residue 997 ASN Chi-restraints excluded: chain G residue 1071 VAL Chi-restraints excluded: chain G residue 1215 LEU Chi-restraints excluded: chain G residue 1356 SER Chi-restraints excluded: chain G residue 1375 VAL Chi-restraints excluded: chain h residue 397 PHE Chi-restraints excluded: chain h residue 476 VAL Chi-restraints excluded: chain h residue 610 MET Chi-restraints excluded: chain u residue 13 TRP Chi-restraints excluded: chain u residue 71 MET Chi-restraints excluded: chain R residue 70 ARG Chi-restraints excluded: chain V residue 12 LEU Chi-restraints excluded: chain V residue 79 ILE Chi-restraints excluded: chain V residue 88 ILE Chi-restraints excluded: chain V residue 107 LEU Chi-restraints excluded: chain V residue 131 VAL Chi-restraints excluded: chain V residue 136 VAL Chi-restraints excluded: chain V residue 290 ARG Chi-restraints excluded: chain V residue 295 VAL Chi-restraints excluded: chain V residue 302 SER Chi-restraints excluded: chain V residue 310 THR Chi-restraints excluded: chain Z residue 143 LEU Chi-restraints excluded: chain Z residue 238 PHE Chi-restraints excluded: chain Z residue 272 CYS Chi-restraints excluded: chain Z residue 283 GLU Chi-restraints excluded: chain Z residue 318 LEU Chi-restraints excluded: chain Z residue 326 VAL Chi-restraints excluded: chain Z residue 473 THR Chi-restraints excluded: chain Z residue 475 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 734 random chunks: chunk 65 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 chunk 573 optimal weight: 8.9990 chunk 667 optimal weight: 0.3980 chunk 114 optimal weight: 9.9990 chunk 448 optimal weight: 8.9990 chunk 314 optimal weight: 8.9990 chunk 663 optimal weight: 40.0000 chunk 270 optimal weight: 0.0000 chunk 577 optimal weight: 9.9990 chunk 388 optimal weight: 50.0000 overall best weight: 5.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 740 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1017 HIS ** A1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 820 HIS ** C1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 HIS ** E 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 820 HIS ** E 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1102 HIS ** F 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 284 GLN F 437 HIS ** F 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 820 HIS ** F1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 820 HIS ** G 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 446 GLN ** R 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 320 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.189738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.173920 restraints weight = 277292.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.172952 restraints weight = 310319.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.173455 restraints weight = 236365.909| |-----------------------------------------------------------------------------| r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5418 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 58361 Z= 0.184 Angle : 0.678 17.088 79551 Z= 0.329 Chirality : 0.044 0.336 9141 Planarity : 0.005 0.065 10399 Dihedral : 4.599 29.850 8089 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.63 % Favored : 92.20 % Rotamer: Outliers : 2.26 % Allowed : 19.44 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.10), residues: 7304 helix: 0.31 (0.11), residues: 2399 sheet: -1.07 (0.17), residues: 960 loop : -1.49 (0.10), residues: 3945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 276 HIS 0.016 0.001 HIS G1064 PHE 0.050 0.001 PHE F 244 TYR 0.021 0.001 TYR R 52 ARG 0.011 0.000 ARG V 156 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15787.49 seconds wall clock time: 275 minutes 39.13 seconds (16539.13 seconds total)