Starting phenix.real_space_refine on Mon Aug 10 01:51:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc0_19041/08_2026/8rc0_19041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc0_19041/08_2026/8rc0_19041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rc0_19041/08_2026/8rc0_19041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc0_19041/08_2026/8rc0_19041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rc0_19041/08_2026/8rc0_19041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc0_19041/08_2026/8rc0_19041.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 106 5.49 5 S 106 5.16 5 C 23912 2.51 5 N 7975 2.21 5 O 8549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40648 Number of models: 1 Model: "" Number of chains: 16 Chain: "F" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 889 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 4, 'GLU:plan': 12, 'GLN:plan1': 5, 'ARG:plan': 8, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 145 Chain: "A" Number of atoms: 16709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2153, 16709 Classifications: {'peptide': 2153} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 324} Link IDs: {'PCIS': 3, 'PTRANS': 122, 'TRANS': 2027} Chain breaks: 7 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1237 Unresolved non-hydrogen angles: 1596 Unresolved non-hydrogen dihedrals: 1045 Unresolved non-hydrogen chiralities: 118 Planarities with less than four sites: {'ARG:plan': 18, 'ASP:plan': 20, 'ASN:plan1': 19, 'GLN:plan1': 15, 'GLU:plan': 24, 'PHE:plan': 13, 'HIS:plan': 10, 'TRP:plan': 11, 'TYR:plan': 9} Unresolved non-hydrogen planarities: 653 Chain: "5" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2192 Classifications: {'RNA': 104} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 14, 'rna3p_pur': 38, 'rna3p_pyr': 43} Link IDs: {'rna2p': 22, 'rna3p': 81} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 516 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain breaks: 1 Chain: "D" Number of atoms: 2941 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 580, 2913 Classifications: {'peptide': 580} Incomplete info: {'backbone_only': 427} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 549} Chain breaks: 7 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2645 Unresolved non-hydrogen dihedrals: 1171 Unresolved non-hydrogen chiralities: 551 Planarities with less than four sites: {'GLU:plan': 42, 'PHE:plan': 14, 'ARG:plan': 32, 'GLN:plan1': 21, 'ASP:plan': 25, 'ASN:plan1': 11, 'TRP:plan': 2, 'HIS:plan': 7, 'TYR:plan': 11} Unresolved non-hydrogen planarities: 804 Conformer: "B" Number of residues, atoms: 580, 2913 Classifications: {'peptide': 580} Incomplete info: {'backbone_only': 427} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 549} Chain breaks: 7 Unresolved chain link angles: 29 Unresolved non-hydrogen bonds: 1849 Unresolved non-hydrogen angles: 2645 Unresolved non-hydrogen dihedrals: 1171 Unresolved non-hydrogen chiralities: 551 Planarities with less than four sites: {'GLU:plan': 42, 'PHE:plan': 14, 'ARG:plan': 32, 'GLN:plan1': 21, 'ASP:plan': 25, 'ASN:plan1': 11, 'TRP:plan': 2, 'HIS:plan': 7, 'TYR:plan': 11} Unresolved non-hydrogen planarities: 804 bond proxies already assigned to first conformer: 2892 Chain: "G" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 1507 Classifications: {'peptide': 306} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 262} Link IDs: {'PTRANS': 10, 'TRANS': 295} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 942 Unresolved non-hydrogen angles: 1215 Unresolved non-hydrogen dihedrals: 801 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'ARG:plan': 17, 'GLN:plan1': 8, 'HIS:plan': 9, 'GLU:plan': 11, 'TYR:plan': 11, 'PHE:plan': 11, 'ASN:plan1': 15, 'ASP:plan': 22, 'TRP:plan': 7, 'GLN%COO:plan1': 1} Unresolved non-hydrogen planarities: 527 Chain: "B" Number of atoms: 6992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1748, 6992 Classifications: {'peptide': 1748} Incomplete info: {'backbone_only': 1664} Link IDs: {'PTRANS': 80, 'TRANS': 1667} Chain breaks: 1 Unresolved chain link angles: 80 Unresolved non-hydrogen bonds: 7347 Unresolved non-hydrogen angles: 10606 Unresolved non-hydrogen dihedrals: 4719 Unresolved non-hydrogen chiralities: 2204 Planarities with less than four sites: {'GLU:plan': 127, 'ARG:plan': 90, 'ASP:plan': 90, 'GLN:plan1': 85, 'PHE:plan': 65, 'HIS:plan': 52, 'ASN:plan1': 70, 'TYR:plan': 61, 'TRP:plan': 19} Unresolved non-hydrogen planarities: 3383 Chain: "i" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 324 Classifications: {'peptide': 81} Incomplete info: {'backbone_only': 77} Link IDs: {'PTRANS': 3, 'TRANS': 77} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 326 Unresolved non-hydrogen angles: 473 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 112 Planarities with less than four sites: {'ARG:plan': 4, 'PHE:plan': 2, 'HIS:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 5, 'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 120 Chain: "k" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 336 Classifications: {'peptide': 84} Incomplete info: {'backbone_only': 78} Link IDs: {'PTRANS': 3, 'TRANS': 80} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 479 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 105 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 7, 'ASN:plan1': 5, 'TYR:plan': 3, 'ARG:plan': 5, 'ASP:plan': 3, 'GLN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 140 Chain: "l" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 308 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 73} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 339 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 98 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 5, 'PHE:plan': 2, 'ARG:plan': 6, 'TYR:plan': 3, 'TRP:plan': 1, 'GLU:plan': 5, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 164 Chain: "m" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 292 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 64} Link IDs: {'PTRANS': 4, 'TRANS': 68} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 291 Unresolved non-hydrogen angles: 421 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 87 Planarities with less than four sites: {'ASN:plan1': 6, 'PHE:plan': 1, 'TRP:plan': 1, 'GLU:plan': 4, 'TYR:plan': 5, 'ASP:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 125 Chain: "n" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 297 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 66} Link IDs: {'PTRANS': 3, 'TRANS': 70} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 288 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'HIS:plan': 2, 'GLU:plan': 5, 'PHE:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 5, 'ARG:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 117 Chain: "j" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 392 Classifications: {'peptide': 98} Incomplete info: {'backbone_only': 95} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 593 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 125 Planarities with less than four sites: {'GLU:plan': 10, 'GLN:plan1': 3, 'ARG:plan': 7, 'PHE:plan': 3, 'ASN:plan1': 10, 'ASP:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 184 Chain: "h" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 292 Classifications: {'peptide': 73} Incomplete info: {'backbone_only': 68} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 312 Unresolved non-hydrogen angles: 439 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASP:plan': 5, 'TYR:plan': 1, 'ARG:plan': 7, 'PHE:plan': 4, 'ASN:plan1': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 6629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 847, 6629 Classifications: {'peptide': 847} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 49, 'TRANS': 797} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N GLU D 464 " occ=0.75 ... (2 atoms not shown) pdb=" O GLU D 464 " occ=0.71 residue: pdb=" N AGLU D 479 " occ=0.25 ... (6 atoms not shown) pdb=" O BGLU D 479 " occ=0.75 residue: pdb=" N AGLU D 581 " occ=0.18 ... (6 atoms not shown) pdb=" O BGLU D 581 " occ=0.82 residue: pdb=" N AGLN D 601 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLN D 601 " occ=0.50 residue: pdb=" N ATHR D 606 " occ=0.34 ... (6 atoms not shown) pdb=" O BTHR D 606 " occ=0.66 residue: pdb=" N AVAL D 733 " occ=0.50 ... (6 atoms not shown) pdb=" O BVAL D 733 " occ=0.50 Time building chain proxies: 7.64, per 1000 atoms: 0.19 Number of scatterers: 40648 At special positions: 0 Unit cell: (143.165, 228.855, 273.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 106 15.00 O 8549 8.00 N 7975 7.00 C 23912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 148 " distance=2.07 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: 3.26 Conformation dependent library (CDL) restraints added in 2.0 seconds 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6888 Finding SS restraints... Secondary structure from input PDB file: 253 helices and 49 sheets defined 43.8% alpha, 16.8% beta 34 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 5.32 Creating SS restraints... Processing helix chain 'F' and resid 67 through 72 removed outlier: 4.057A pdb=" N VAL F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU F 72 " --> pdb=" O SER F 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 72' Processing helix chain 'F' and resid 92 through 99 Processing helix chain 'F' and resid 117 through 122 removed outlier: 3.627A pdb=" N ASN F 122 " --> pdb=" O SER F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 170 through 178 Processing helix chain 'F' and resid 196 through 212 Processing helix chain 'F' and resid 216 through 220 Processing helix chain 'F' and resid 221 through 233 Processing helix chain 'A' and resid 62 through 72 removed outlier: 4.344A pdb=" N VAL A 66 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.843A pdb=" N ALA A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A 92 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 105 Processing helix chain 'A' and resid 136 through 156 removed outlier: 3.512A pdb=" N ARG A 156 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 231 through 242 Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 259 through 269 Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.725A pdb=" N LYS A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 404 Processing helix chain 'A' and resid 422 through 424 No H-bonds generated for 'chain 'A' and resid 422 through 424' Processing helix chain 'A' and resid 440 through 460 Processing helix chain 'A' and resid 471 through 479 removed outlier: 3.502A pdb=" N THR A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 510 Processing helix chain 'A' and resid 533 through 537 Processing helix chain 'A' and resid 541 through 567 removed outlier: 3.952A pdb=" N HIS A 545 " --> pdb=" O GLY A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 584 Processing helix chain 'A' and resid 590 through 594 removed outlier: 3.790A pdb=" N ARG A 593 " --> pdb=" O GLY A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 596 No H-bonds generated for 'chain 'A' and resid 595 through 596' Processing helix chain 'A' and resid 597 through 617 removed outlier: 4.169A pdb=" N GLN A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 614 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A 615 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 656 removed outlier: 3.691A pdb=" N ARG A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 641 " --> pdb=" O TRP A 637 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY A 643 " --> pdb=" O PHE A 639 " (cutoff:3.500A) Proline residue: A 646 - end of helix Processing helix chain 'A' and resid 681 through 697 removed outlier: 3.708A pdb=" N MET A 696 " --> pdb=" O ASP A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 722 Processing helix chain 'A' and resid 732 through 764 Processing helix chain 'A' and resid 768 through 798 Processing helix chain 'A' and resid 802 through 820 Processing helix chain 'A' and resid 834 through 850 removed outlier: 3.624A pdb=" N ALA A 849 " --> pdb=" O ARG A 845 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR A 850 " --> pdb=" O LEU A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 873 Processing helix chain 'A' and resid 873 through 887 removed outlier: 3.651A pdb=" N ALA A 877 " --> pdb=" O ASN A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 934 Processing helix chain 'A' and resid 947 through 961 removed outlier: 3.672A pdb=" N TYR A 953 " --> pdb=" O PRO A 949 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1001 removed outlier: 4.309A pdb=" N LEU A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A1001 " --> pdb=" O LEU A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1002 through 1013 Processing helix chain 'A' and resid 1036 through 1063 removed outlier: 6.786A pdb=" N LEU A1055 " --> pdb=" O LEU A1051 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N HIS A1056 " --> pdb=" O VAL A1052 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG A1057 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1081 Processing helix chain 'A' and resid 1102 through 1117 Processing helix chain 'A' and resid 1143 through 1161 removed outlier: 3.514A pdb=" N ARG A1160 " --> pdb=" O ASP A1156 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A1161 " --> pdb=" O ILE A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1173 Processing helix chain 'A' and resid 1233 through 1250 Processing helix chain 'A' and resid 1255 through 1274 removed outlier: 3.546A pdb=" N ILE A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1281 removed outlier: 4.203A pdb=" N VAL A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1304 Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 3.531A pdb=" N TYR A1317 " --> pdb=" O PRO A1313 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A1318 " --> pdb=" O VAL A1314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1313 through 1318' Processing helix chain 'A' and resid 1319 through 1323 Processing helix chain 'A' and resid 1336 through 1341 removed outlier: 3.789A pdb=" N ARG A1341 " --> pdb=" O SER A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1367 through 1371 Processing helix chain 'A' and resid 1374 through 1400 Processing helix chain 'A' and resid 1408 through 1412 removed outlier: 3.814A pdb=" N TRP A1412 " --> pdb=" O GLU A1409 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1425 removed outlier: 3.766A pdb=" N GLN A1424 " --> pdb=" O THR A1421 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS A1425 " --> pdb=" O LEU A1422 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1431 Processing helix chain 'A' and resid 1435 through 1442 removed outlier: 3.508A pdb=" N ARG A1439 " --> pdb=" O GLY A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1446 Processing helix chain 'A' and resid 1457 through 1462 Processing helix chain 'A' and resid 1467 through 1479 removed outlier: 3.591A pdb=" N GLY A1479 " --> pdb=" O ILE A1475 " (cutoff:3.500A) Processing helix chain 'A' and resid 1479 through 1487 removed outlier: 4.186A pdb=" N HIS A1487 " --> pdb=" O GLY A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1494 Processing helix chain 'A' and resid 1531 through 1538 Processing helix chain 'A' and resid 1539 through 1542 Processing helix chain 'A' and resid 1566 through 1576 Processing helix chain 'A' and resid 1580 through 1600 Processing helix chain 'A' and resid 1617 through 1621 Processing helix chain 'A' and resid 1675 through 1688 Processing helix chain 'A' and resid 1721 through 1737 Processing helix chain 'A' and resid 1737 through 1752 Processing helix chain 'A' and resid 1767 through 1773 removed outlier: 3.901A pdb=" N PHE A1772 " --> pdb=" O GLY A1769 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A1773 " --> pdb=" O GLU A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1823 through 1827 Processing helix chain 'A' and resid 1833 through 1852 removed outlier: 3.569A pdb=" N ALA A1837 " --> pdb=" O LEU A1833 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TRP A1839 " --> pdb=" O GLN A1835 " (cutoff:3.500A) Processing helix chain 'A' and resid 1868 through 1876 Processing helix chain 'A' and resid 1893 through 1899 removed outlier: 3.683A pdb=" N LEU A1897 " --> pdb=" O PHE A1893 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1909 Processing helix chain 'A' and resid 1922 through 1926 removed outlier: 3.627A pdb=" N LYS A1925 " --> pdb=" O ASP A1922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1928 through 1946 Processing helix chain 'A' and resid 1946 through 1955 removed outlier: 3.506A pdb=" N ALA A1950 " --> pdb=" O ASN A1946 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A1955 " --> pdb=" O LYS A1951 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1995 Processing helix chain 'A' and resid 2003 through 2013 Processing helix chain 'A' and resid 2071 through 2081 Processing helix chain 'A' and resid 2082 through 2087 Processing helix chain 'A' and resid 2108 through 2117 Processing helix chain 'A' and resid 2189 through 2203 Processing helix chain 'A' and resid 2231 through 2241 Processing helix chain 'A' and resid 2252 through 2254 No H-bonds generated for 'chain 'A' and resid 2252 through 2254' Processing helix chain 'A' and resid 2284 through 2288 Processing helix chain 'A' and resid 2306 through 2310 removed outlier: 3.618A pdb=" N ARG A2310 " --> pdb=" O GLU A2307 " (cutoff:3.500A) Processing helix chain 'A' and resid 2311 through 2316 removed outlier: 3.785A pdb=" N ASN A2316 " --> pdb=" O SER A2312 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 114 removed outlier: 3.504A pdb=" N ASP E 113 " --> pdb=" O ASP E 109 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU E 114 " --> pdb=" O LYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 127 Processing helix chain 'E' and resid 138 through 150 removed outlier: 5.095A pdb=" N ASP E 144 " --> pdb=" O GLN E 140 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LEU E 145 " --> pdb=" O GLN E 141 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 152 No H-bonds generated for 'chain 'E' and resid 151 through 152' Processing helix chain 'E' and resid 153 through 157 Processing helix chain 'D' and resid 165 through 201 Processing helix chain 'D' and resid 244 through 255 Processing helix chain 'D' and resid 277 through 281 removed outlier: 3.700A pdb=" N ASP D 281 " --> pdb=" O ALA D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 301 Processing helix chain 'D' and resid 308 through 316 Processing helix chain 'D' and resid 318 through 328 removed outlier: 3.605A pdb=" N ASP D 322 " --> pdb=" O ARG D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 354 removed outlier: 3.590A pdb=" N ASP D 354 " --> pdb=" O GLN D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 377 Processing helix chain 'D' and resid 399 through 410 Processing helix chain 'D' and resid 415 through 426 Proline residue: D 423 - end of helix Processing helix chain 'D' and resid 440 through 455 Proline residue: D 448 - end of helix Processing helix chain 'D' and resid 457 through 462 Processing helix chain 'D' and resid 477 through 493 Processing helix chain 'D' and resid 507 through 518 removed outlier: 3.619A pdb=" N MET D 517 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 535 Processing helix chain 'D' and resid 550 through 557 Processing helix chain 'D' and resid 559 through 569 removed outlier: 3.809A pdb=" N HIS D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 575 removed outlier: 5.998A pdb=" N SER D 573 " --> pdb=" O MET D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 583 Processing helix chain 'D' and resid 584 through 594 Processing helix chain 'D' and resid 595 through 598 Processing helix chain 'D' and resid 610 through 621 Processing helix chain 'D' and resid 634 through 639 removed outlier: 3.649A pdb=" N ARG D 638 " --> pdb=" O LYS D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 649 No H-bonds generated for 'chain 'D' and resid 647 through 649' Processing helix chain 'D' and resid 650 through 661 Processing helix chain 'D' and resid 673 through 687 Processing helix chain 'D' and resid 704 through 712 Processing helix chain 'D' and resid 744 through 753 Processing helix chain 'D' and resid 754 through 756 No H-bonds generated for 'chain 'D' and resid 754 through 756' Processing helix chain 'D' and resid 769 through 774 removed outlier: 3.511A pdb=" N SER D 773 " --> pdb=" O LYS D 770 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ALA D 774 " --> pdb=" O GLU D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 785 Processing helix chain 'D' and resid 793 through 797 Processing helix chain 'D' and resid 798 through 802 removed outlier: 3.640A pdb=" N GLN D 802 " --> pdb=" O PRO D 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 422 removed outlier: 3.671A pdb=" N HIS B 421 " --> pdb=" O GLN B 418 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 422 " --> pdb=" O GLY B 419 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 418 through 422' Processing helix chain 'B' and resid 468 through 473 removed outlier: 4.280A pdb=" N ALA B 473 " --> pdb=" O LYS B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 488 Processing helix chain 'B' and resid 488 through 494 Processing helix chain 'B' and resid 508 through 522 removed outlier: 4.098A pdb=" N VAL B 512 " --> pdb=" O GLY B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 559 removed outlier: 3.899A pdb=" N GLY B 553 " --> pdb=" O GLN B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 589 through 600 Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 616 through 622 removed outlier: 3.554A pdb=" N LEU B 620 " --> pdb=" O ILE B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 643 removed outlier: 3.524A pdb=" N LEU B 628 " --> pdb=" O ARG B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 665 Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 696 through 715 removed outlier: 3.681A pdb=" N HIS B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 727 through 745 removed outlier: 3.560A pdb=" N GLY B 732 " --> pdb=" O ARG B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 769 removed outlier: 3.514A pdb=" N VAL B 761 " --> pdb=" O ALA B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 778 removed outlier: 3.874A pdb=" N LEU B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 803 Processing helix chain 'B' and resid 812 through 819 removed outlier: 4.327A pdb=" N ALA B 816 " --> pdb=" O THR B 812 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TRP B 817 " --> pdb=" O ALA B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 845 through 854 Processing helix chain 'B' and resid 875 through 883 removed outlier: 3.559A pdb=" N TYR B 879 " --> pdb=" O GLU B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 907 Processing helix chain 'B' and resid 912 through 922 removed outlier: 3.616A pdb=" N TYR B 922 " --> pdb=" O ASN B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 932 removed outlier: 3.641A pdb=" N ILE B 927 " --> pdb=" O ALA B 923 " (cutoff:3.500A) Processing helix chain 'B' and resid 939 through 945 Processing helix chain 'B' and resid 949 through 967 removed outlier: 3.598A pdb=" N ARG B 953 " --> pdb=" O LEU B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 992 Processing helix chain 'B' and resid 994 through 1005 Processing helix chain 'B' and resid 1010 through 1020 Processing helix chain 'B' and resid 1021 through 1025 Processing helix chain 'B' and resid 1030 through 1032 No H-bonds generated for 'chain 'B' and resid 1030 through 1032' Processing helix chain 'B' and resid 1033 through 1042 Processing helix chain 'B' and resid 1054 through 1069 Processing helix chain 'B' and resid 1074 through 1103 removed outlier: 4.420A pdb=" N ARG B1090 " --> pdb=" O GLN B1086 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1121 Processing helix chain 'B' and resid 1127 through 1132 Processing helix chain 'B' and resid 1136 through 1146 Processing helix chain 'B' and resid 1149 through 1154 Processing helix chain 'B' and resid 1157 through 1165 Processing helix chain 'B' and resid 1167 through 1181 removed outlier: 4.576A pdb=" N LYS B1172 " --> pdb=" O PRO B1168 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N THR B1173 " --> pdb=" O LYS B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1312 Processing helix chain 'B' and resid 1314 through 1319 Processing helix chain 'B' and resid 1329 through 1340 removed outlier: 4.241A pdb=" N ASN B1337 " --> pdb=" O THR B1333 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N THR B1338 " --> pdb=" O GLN B1334 " (cutoff:3.500A) Processing helix chain 'B' and resid 1355 through 1371 removed outlier: 3.695A pdb=" N CYS B1359 " --> pdb=" O GLY B1355 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B1371 " --> pdb=" O MET B1367 " (cutoff:3.500A) Processing helix chain 'B' and resid 1382 through 1398 Processing helix chain 'B' and resid 1411 through 1422 removed outlier: 4.252A pdb=" N LYS B1417 " --> pdb=" O SER B1413 " (cutoff:3.500A) Processing helix chain 'B' and resid 1428 through 1437 removed outlier: 3.608A pdb=" N ILE B1434 " --> pdb=" O GLU B1430 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B1435 " --> pdb=" O LYS B1431 " (cutoff:3.500A) Processing helix chain 'B' and resid 1442 through 1447 removed outlier: 3.710A pdb=" N GLN B1446 " --> pdb=" O ARG B1442 " (cutoff:3.500A) Processing helix chain 'B' and resid 1456 through 1461 removed outlier: 3.511A pdb=" N ILE B1459 " --> pdb=" O VAL B1456 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B1460 " --> pdb=" O HIS B1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 1464 through 1479 Processing helix chain 'B' and resid 1496 through 1504 removed outlier: 3.732A pdb=" N VAL B1500 " --> pdb=" O ASN B1496 " (cutoff:3.500A) Processing helix chain 'B' and resid 1515 through 1519 removed outlier: 4.139A pdb=" N ARG B1519 " --> pdb=" O PRO B1516 " (cutoff:3.500A) Processing helix chain 'B' and resid 1534 through 1542 Processing helix chain 'B' and resid 1542 through 1554 Processing helix chain 'B' and resid 1565 through 1583 removed outlier: 3.506A pdb=" N THR B1569 " --> pdb=" O SER B1565 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG B1570 " --> pdb=" O ARG B1566 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B1571 " --> pdb=" O LYS B1567 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B1583 " --> pdb=" O THR B1579 " (cutoff:3.500A) Processing helix chain 'B' and resid 1597 through 1602 Processing helix chain 'B' and resid 1606 through 1615 removed outlier: 3.684A pdb=" N ASN B1615 " --> pdb=" O GLU B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1625 through 1638 Processing helix chain 'B' and resid 1649 through 1651 No H-bonds generated for 'chain 'B' and resid 1649 through 1651' Processing helix chain 'B' and resid 1680 through 1690 Processing helix chain 'B' and resid 1710 through 1720 removed outlier: 4.252A pdb=" N TYR B1719 " --> pdb=" O LYS B1715 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B1720 " --> pdb=" O LYS B1716 " (cutoff:3.500A) Processing helix chain 'B' and resid 1732 through 1742 Processing helix chain 'B' and resid 1747 through 1756 Processing helix chain 'B' and resid 1758 through 1765 removed outlier: 3.733A pdb=" N ARG B1762 " --> pdb=" O THR B1758 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR B1765 " --> pdb=" O TYR B1761 " (cutoff:3.500A) Processing helix chain 'B' and resid 1767 through 1772 removed outlier: 3.620A pdb=" N ASN B1772 " --> pdb=" O ASN B1769 " (cutoff:3.500A) Processing helix chain 'B' and resid 1777 through 1799 Processing helix chain 'B' and resid 1813 through 1822 Processing helix chain 'B' and resid 1825 through 1836 Processing helix chain 'B' and resid 1841 through 1851 removed outlier: 4.424A pdb=" N GLU B1847 " --> pdb=" O ARG B1843 " (cutoff:3.500A) Processing helix chain 'B' and resid 1852 through 1856 Processing helix chain 'B' and resid 1864 through 1872 removed outlier: 3.680A pdb=" N LEU B1868 " --> pdb=" O GLU B1864 " (cutoff:3.500A) Processing helix chain 'B' and resid 1886 through 1901 removed outlier: 3.534A pdb=" N LYS B1890 " --> pdb=" O ASP B1886 " (cutoff:3.500A) Processing helix chain 'B' and resid 1905 through 1934 removed outlier: 3.509A pdb=" N GLU B1914 " --> pdb=" O SER B1910 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B1918 " --> pdb=" O GLU B1914 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B1920 " --> pdb=" O LEU B1916 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ARG B1921 " --> pdb=" O SER B1917 " (cutoff:3.500A) Processing helix chain 'B' and resid 1935 through 1952 Processing helix chain 'B' and resid 1967 through 1976 removed outlier: 3.740A pdb=" N ILE B1971 " --> pdb=" O THR B1967 " (cutoff:3.500A) Processing helix chain 'B' and resid 1982 through 1987 removed outlier: 3.605A pdb=" N GLU B1987 " --> pdb=" O PHE B1983 " (cutoff:3.500A) Processing helix chain 'B' and resid 1989 through 1995 Processing helix chain 'B' and resid 2000 through 2014 removed outlier: 4.088A pdb=" N ALA B2005 " --> pdb=" O ASP B2001 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B2009 " --> pdb=" O ALA B2005 " (cutoff:3.500A) Processing helix chain 'i' and resid 3 through 9 removed outlier: 3.548A pdb=" N LEU i 7 " --> pdb=" O LEU i 3 " (cutoff:3.500A) Processing helix chain 'i' and resid 75 through 79 Processing helix chain 'k' and resid 4 through 12 Processing helix chain 'k' and resid 74 through 80 Processing helix chain 'l' and resid 16 through 28 Processing helix chain 'm' and resid 6 through 14 Processing helix chain 'n' and resid 9 through 13 Processing helix chain 'j' and resid 18 through 24 removed outlier: 3.510A pdb=" N GLU j 22 " --> pdb=" O LYS j 18 " (cutoff:3.500A) Processing helix chain 'j' and resid 29 through 39 removed outlier: 3.635A pdb=" N THR j 33 " --> pdb=" O LEU j 29 " (cutoff:3.500A) Processing helix chain 'j' and resid 102 through 104 No H-bonds generated for 'chain 'j' and resid 102 through 104' Processing helix chain 'h' and resid 7 through 11 Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 142 through 153 Processing helix chain 'C' and resid 172 through 178 Processing helix chain 'C' and resid 208 through 210 No H-bonds generated for 'chain 'C' and resid 208 through 210' Processing helix chain 'C' and resid 211 through 220 removed outlier: 3.839A pdb=" N VAL C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 249 Processing helix chain 'C' and resid 260 through 266 removed outlier: 3.769A pdb=" N ILE C 264 " --> pdb=" O ILE C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 292 Processing helix chain 'C' and resid 312 through 315 Processing helix chain 'C' and resid 319 through 331 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 341 through 343 No H-bonds generated for 'chain 'C' and resid 341 through 343' Processing helix chain 'C' and resid 367 through 373 Processing helix chain 'C' and resid 373 through 387 removed outlier: 3.509A pdb=" N LEU C 377 " --> pdb=" O ILE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 removed outlier: 3.786A pdb=" N THR C 395 " --> pdb=" O SER C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 Processing helix chain 'C' and resid 427 through 438 removed outlier: 3.554A pdb=" N VAL C 431 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 453 Processing helix chain 'C' and resid 460 through 465 Processing helix chain 'C' and resid 596 through 598 No H-bonds generated for 'chain 'C' and resid 596 through 598' Processing helix chain 'C' and resid 599 through 614 removed outlier: 3.575A pdb=" N MET C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 647 Processing helix chain 'C' and resid 696 through 702 Processing helix chain 'C' and resid 710 through 723 Processing helix chain 'C' and resid 725 through 730 Processing helix chain 'C' and resid 755 through 760 Processing helix chain 'C' and resid 762 through 777 removed outlier: 3.899A pdb=" N GLN C 768 " --> pdb=" O ASP C 764 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 823 removed outlier: 3.512A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 852 removed outlier: 4.098A pdb=" N ARG C 852 " --> pdb=" O THR C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 881 removed outlier: 4.093A pdb=" N PHE C 881 " --> pdb=" O ILE C 878 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 878 through 881' Processing helix chain 'C' and resid 882 through 891 Processing helix chain 'C' and resid 925 through 927 No H-bonds generated for 'chain 'C' and resid 925 through 927' Processing helix chain 'C' and resid 928 through 942 removed outlier: 3.662A pdb=" N GLU C 932 " --> pdb=" O HIS C 928 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 135 Processing sheet with id=AA3, first strand: chain 'A' and resid 228 through 229 Processing sheet with id=AA4, first strand: chain 'A' and resid 516 through 518 Processing sheet with id=AA5, first strand: chain 'A' and resid 905 through 910 removed outlier: 3.843A pdb=" N VAL A 906 " --> pdb=" O MET A 899 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL A 894 " --> pdb=" O ASN A1018 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1085 through 1090 removed outlier: 5.308A pdb=" N ILE A1085 " --> pdb=" O ARG A1100 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ARG A1100 " --> pdb=" O ILE A1085 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE A1095 " --> pdb=" O SER A 979 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1185 through 1189 Processing sheet with id=AA8, first strand: chain 'A' and resid 1342 through 1346 Processing sheet with id=AA9, first strand: chain 'A' and resid 1553 through 1554 removed outlier: 4.041A pdb=" N VAL A1553 " --> pdb=" O MET A1562 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A1562 " --> pdb=" O VAL A1553 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1608 through 1611 removed outlier: 12.437A pdb=" N ILE A1629 " --> pdb=" O GLN A1665 " (cutoff:3.500A) removed outlier: 11.039A pdb=" N GLN A1665 " --> pdb=" O ILE A1629 " (cutoff:3.500A) removed outlier: 11.505A pdb=" N LEU A1631 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 11.362A pdb=" N ASP A1663 " --> pdb=" O LEU A1631 " (cutoff:3.500A) removed outlier: 11.331A pdb=" N ALA A1633 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 12.351A pdb=" N TRP A1661 " --> pdb=" O ALA A1633 " (cutoff:3.500A) removed outlier: 10.037A pdb=" N TYR A1635 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LYS A1659 " --> pdb=" O TYR A1635 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A1639 " --> pdb=" O THR A1655 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR A1655 " --> pdb=" O VAL A1639 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL A1701 " --> pdb=" O LYS A1659 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N TRP A1661 " --> pdb=" O VAL A1701 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ILE A1703 " --> pdb=" O TRP A1661 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ASP A1663 " --> pdb=" O ILE A1703 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ILE A1705 " --> pdb=" O ASP A1663 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN A1665 " --> pdb=" O ILE A1705 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1883 through 1886 removed outlier: 6.525A pdb=" N TRP A1778 " --> pdb=" O ILE A1862 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1787 through 1793 removed outlier: 4.472A pdb=" N ARG A1787 " --> pdb=" O ILE A1803 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A1793 " --> pdb=" O ASN A1797 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASN A1797 " --> pdb=" O THR A1793 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2090 through 2092 removed outlier: 6.418A pdb=" N GLY A2130 " --> pdb=" O PRO A2174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A2176 " --> pdb=" O LEU A2128 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A2131 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE A2142 " --> pdb=" O VAL A2131 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N THR A2103 " --> pdb=" O LYS A2140 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE A2142 " --> pdb=" O THR A2103 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE A2105 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N CYS A2144 " --> pdb=" O ILE A2105 " (cutoff:3.500A) removed outlier: 11.664A pdb=" N VAL A2146 " --> pdb=" O PRO A2107 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A2264 " --> pdb=" O LEU A2106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2256 through 2258 removed outlier: 6.418A pdb=" N GLY A2130 " --> pdb=" O PRO A2174 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY A2176 " --> pdb=" O LEU A2128 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A2131 " --> pdb=" O ILE A2142 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE A2142 " --> pdb=" O VAL A2131 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2151 through 2152 removed outlier: 3.948A pdb=" N TRP A2151 " --> pdb=" O HIS A2158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 379 through 382 removed outlier: 6.371A pdb=" N VAL D 546 " --> pdb=" O VAL D 603 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N PHE D 605 " --> pdb=" O VAL D 546 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU D 548 " --> pdb=" O PHE D 605 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 640 through 645 removed outlier: 6.281A pdb=" N ILE D 668 " --> pdb=" O VAL D 737 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N CYS D 692 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 61 through 63 Processing sheet with id=AC1, first strand: chain 'G' and resid 71 through 74 removed outlier: 3.644A pdb=" N ALA G 103 " --> pdb=" O LEU G 92 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ASN G 94 " --> pdb=" O ASN G 101 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN G 101 " --> pdb=" O ASN G 94 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 112 through 117 removed outlier: 6.571A pdb=" N ALA G 127 " --> pdb=" O MET G 113 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N LEU G 115 " --> pdb=" O PHE G 125 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE G 125 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR G 117 " --> pdb=" O MET G 123 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N MET G 123 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP G 137 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG G 143 " --> pdb=" O ASP G 137 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 154 through 159 removed outlier: 6.419A pdb=" N GLY G 170 " --> pdb=" O ASN G 155 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N CYS G 157 " --> pdb=" O CYS G 168 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N CYS G 168 " --> pdb=" O CYS G 157 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU G 166 " --> pdb=" O PRO G 159 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER G 171 " --> pdb=" O THR G 175 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N THR G 175 " --> pdb=" O SER G 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN G 188 " --> pdb=" O LEU G 178 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ASP G 180 " --> pdb=" O ALA G 186 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA G 186 " --> pdb=" O ASP G 180 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 196 through 201 removed outlier: 4.443A pdb=" N GLY G 212 " --> pdb=" O ASP G 216 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASP G 216 " --> pdb=" O GLY G 212 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE G 217 " --> pdb=" O THR G 230 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR G 230 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL G 219 " --> pdb=" O THR G 228 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 238 through 243 removed outlier: 3.798A pdb=" N ALA G 254 " --> pdb=" O THR G 258 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR G 258 " --> pdb=" O ALA G 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS G 275 " --> pdb=" O VAL G 261 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 291 through 293 removed outlier: 3.611A pdb=" N ALA G 302 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N TYR G 310 " --> pdb=" O ALA G 302 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ASP G 313 " --> pdb=" O ILE G 319 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ILE G 319 " --> pdb=" O ASP G 313 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 330 through 335 Processing sheet with id=AC8, first strand: chain 'B' and resid 436 through 438 removed outlier: 6.321A pdb=" N VAL B 826 " --> pdb=" O ILE B 868 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE B 870 " --> pdb=" O VAL B 826 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE B 828 " --> pdb=" O ILE B 870 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N SER B 872 " --> pdb=" O ILE B 828 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.252A pdb=" N ALA B 567 " --> pdb=" O VAL B 587 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ILE B 538 " --> pdb=" O ILE B 586 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N CYS B 588 " --> pdb=" O ILE B 538 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR B 540 " --> pdb=" O CYS B 588 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LYS B 537 " --> pdb=" O VAL B 609 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 611 " --> pdb=" O LYS B 537 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 499 " --> pdb=" O GLY B 650 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N SER B 652 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU B 501 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 832 through 835 removed outlier: 3.570A pdb=" N ARG B 840 " --> pdb=" O SER B 835 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 970 through 972 Processing sheet with id=AD3, first strand: chain 'B' and resid 1184 through 1191 Processing sheet with id=AD4, first strand: chain 'B' and resid 1233 through 1242 Processing sheet with id=AD5, first strand: chain 'B' and resid 1405 through 1407 removed outlier: 6.953A pdb=" N CYS B1376 " --> pdb=" O ILE B1425 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N SER B1427 " --> pdb=" O CYS B1376 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N TYR B1378 " --> pdb=" O SER B1427 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL B1377 " --> pdb=" O VAL B1452 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASP B1454 " --> pdb=" O VAL B1377 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B1379 " --> pdb=" O ASP B1454 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE B1347 " --> pdb=" O PHE B1512 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1523 through 1530 removed outlier: 6.315A pdb=" N ILE B1560 " --> pdb=" O ILE B1662 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N MET B1664 " --> pdb=" O ILE B1560 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N PHE B1562 " --> pdb=" O MET B1664 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1667 through 1670 Processing sheet with id=AD8, first strand: chain 'B' and resid 1802 through 1805 Processing sheet with id=AD9, first strand: chain 'B' and resid 2017 through 2018 Processing sheet with id=AE1, first strand: chain 'B' and resid 2017 through 2018 removed outlier: 3.869A pdb=" N ALA B2088 " --> pdb=" O LEU B2041 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 2076 through 2082 removed outlier: 3.753A pdb=" N GLN B2118 " --> pdb=" O PHE B2108 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'i' and resid 13 through 19 removed outlier: 3.763A pdb=" N GLU i 13 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR i 28 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA i 42 " --> pdb=" O THR i 28 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N THR i 30 " --> pdb=" O LEU i 40 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU i 40 " --> pdb=" O THR i 30 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL i 32 " --> pdb=" O THR i 38 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR i 38 " --> pdb=" O VAL i 32 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU i 56 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LYS i 44 " --> pdb=" O GLN i 54 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN i 54 " --> pdb=" O LYS i 44 " (cutoff:3.500A) removed outlier: 14.134A pdb=" N LEU i 55 " --> pdb=" O GLY h 84 " (cutoff:3.500A) removed outlier: 12.257A pdb=" N GLY h 84 " --> pdb=" O LEU i 55 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N THR i 57 " --> pdb=" O VAL h 82 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL h 82 " --> pdb=" O THR i 57 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG h 16 " --> pdb=" O GLU h 83 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N THR h 30 " --> pdb=" O ASP h 44 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASP h 44 " --> pdb=" O THR h 30 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N LYS h 32 " --> pdb=" O LEU h 42 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU h 42 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE h 34 " --> pdb=" O LEU h 40 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU h 40 " --> pdb=" O PHE h 34 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N GLY h 68 " --> pdb=" O ASP h 44 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP h 46 " --> pdb=" O VAL h 66 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N VAL h 66 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE h 48 " --> pdb=" O LYS h 64 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N LYS h 64 " --> pdb=" O PHE h 48 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LEU h 69 " --> pdb=" O LEU k 73 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLU k 21 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU k 71 " --> pdb=" O THR k 19 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR k 19 " --> pdb=" O LEU k 71 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU k 73 " --> pdb=" O ILE k 17 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE k 17 " --> pdb=" O LEU k 73 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG k 29 " --> pdb=" O THR k 47 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LYS k 31 " --> pdb=" O ASN k 45 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ASN k 45 " --> pdb=" O LYS k 31 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER k 44 " --> pdb=" O GLN k 60 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLN k 60 " --> pdb=" O SER k 44 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLN k 60 " --> pdb=" O ALA n 72 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET n 69 " --> pdb=" O LYS n 20 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ILE n 30 " --> pdb=" O GLU n 44 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N GLU n 44 " --> pdb=" O ILE n 30 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ARG n 32 " --> pdb=" O ILE n 42 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE n 42 " --> pdb=" O ARG n 32 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N PHE n 34 " --> pdb=" O LEU n 40 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LEU n 40 " --> pdb=" O PHE n 34 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL n 41 " --> pdb=" O VAL n 61 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL n 61 " --> pdb=" O VAL n 41 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASP n 43 " --> pdb=" O MET n 59 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N MET n 59 " --> pdb=" O ASP n 43 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N CYS n 45 " --> pdb=" O ILE n 57 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU l 86 " --> pdb=" O TRP l 34 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N CYS l 46 " --> pdb=" O ASP l 60 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASP l 60 " --> pdb=" O CYS l 46 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE l 48 " --> pdb=" O LEU l 58 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N LEU l 58 " --> pdb=" O ILE l 48 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL l 57 " --> pdb=" O MET l 78 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET l 78 " --> pdb=" O VAL l 57 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ASP l 59 " --> pdb=" O ARG l 76 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ALA l 61 " --> pdb=" O LEU l 74 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS m 22 " --> pdb=" O LEU m 70 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE m 72 " --> pdb=" O MET m 20 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N MET m 20 " --> pdb=" O ILE m 72 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N MET m 27 " --> pdb=" O LEU m 23 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU m 28 " --> pdb=" O GLU m 49 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLU m 49 " --> pdb=" O GLU m 28 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LYS m 30 " --> pdb=" O THR m 47 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR m 47 " --> pdb=" O LYS m 30 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N TYR m 32 " --> pdb=" O ALA m 45 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA m 45 " --> pdb=" O TYR m 32 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLN m 43 " --> pdb=" O VAL m 34 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN m 46 " --> pdb=" O GLY m 60 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY m 60 " --> pdb=" O ASN m 46 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N GLU m 48 " --> pdb=" O HIS m 58 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N HIS m 58 " --> pdb=" O GLU m 48 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N TYR m 50 " --> pdb=" O SER m 56 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER m 56 " --> pdb=" O TYR m 50 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU m 61 " --> pdb=" O ARG j 111 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN j 45 " --> pdb=" O ILE j 107 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N VAL j 109 " --> pdb=" O LEU j 43 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LEU j 43 " --> pdb=" O VAL j 109 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS j 50 " --> pdb=" O CYS j 46 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG j 55 " --> pdb=" O ASN j 69 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ASN j 69 " --> pdb=" O ARG j 55 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS j 57 " --> pdb=" O LEU j 67 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU j 67 " --> pdb=" O LYS j 57 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL j 66 " --> pdb=" O PHE j 100 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N PHE j 100 " --> pdb=" O VAL j 66 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU j 68 " --> pdb=" O LYS j 98 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LYS j 98 " --> pdb=" O GLU j 68 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'k' and resid 34 through 35 removed outlier: 3.743A pdb=" N GLU k 34 " --> pdb=" O GLN k 42 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 184 through 191 removed outlier: 9.119A pdb=" N GLY C 224 " --> pdb=" O ILE C 129 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN C 131 " --> pdb=" O GLY C 224 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N VAL C 226 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR C 133 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N PHE C 228 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS C 135 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL C 225 " --> pdb=" O THR C 254 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N CYS C 256 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU C 227 " --> pdb=" O CYS C 256 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 348 through 350 removed outlier: 3.502A pdb=" N LYS C 355 " --> pdb=" O ASN C 350 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 523 through 526 removed outlier: 6.273A pdb=" N MET C 475 " --> pdb=" O LEU C 497 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE C 493 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N MET C 481 " --> pdb=" O HIS C 491 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N HIS C 491 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N TRP C 549 " --> pdb=" O SER C 533 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N SER C 533 " --> pdb=" O TRP C 549 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU C 530 " --> pdb=" O VAL C 541 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 500 through 502 Processing sheet with id=AE9, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.809A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 618 through 621 removed outlier: 3.809A pdb=" N THR C 618 " --> pdb=" O LEU C 630 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N HIS C 627 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 783 through 784 removed outlier: 6.461A pdb=" N PHE C 874 " --> pdb=" O VAL C 857 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL C 857 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 783 through 784 removed outlier: 5.399A pdb=" N PHE C 833 " --> pdb=" O PHE C 901 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE C 901 " --> pdb=" O PHE C 833 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLU C 835 " --> pdb=" O SER C 899 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N SER C 899 " --> pdb=" O GLU C 835 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N GLN C 837 " --> pdb=" O SER C 897 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N SER C 897 " --> pdb=" O GLN C 837 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 674 through 677 removed outlier: 6.379A pdb=" N ILE C 744 " --> pdb=" O PHE C 789 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N ILE C 791 " --> pdb=" O ILE C 744 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL C 746 " --> pdb=" O ILE C 791 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASN C 743 " --> pdb=" O PHE C 735 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N PHE C 735 " --> pdb=" O ASN C 743 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU C 745 " --> pdb=" O TRP C 733 " (cutoff:3.500A) 2312 hydrogen bonds defined for protein. 6555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 83 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 17.49 Time building geometry restraints manager: 4.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 7492 1.29 - 1.43: 11193 1.43 - 1.56: 22429 1.56 - 1.69: 211 1.69 - 1.83: 174 Bond restraints: 41499 Sorted by residual: bond pdb=" C CYS C 144 " pdb=" O CYS C 144 " ideal model delta sigma weight residual 1.236 1.158 0.079 1.47e-02 4.63e+03 2.86e+01 bond pdb=" C LYS C 142 " pdb=" O LYS C 142 " ideal model delta sigma weight residual 1.236 1.279 -0.043 1.22e-02 6.72e+03 1.25e+01 bond pdb=" C CYS C 148 " pdb=" O CYS C 148 " ideal model delta sigma weight residual 1.236 1.278 -0.041 1.25e-02 6.40e+03 1.09e+01 bond pdb=" N LEU C 149 " pdb=" CA LEU C 149 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.23e-02 6.61e+03 1.06e+01 bond pdb=" N LYS C 142 " pdb=" CA LYS C 142 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.26e-02 6.30e+03 8.72e+00 ... (remaining 41494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.06: 55471 4.06 - 8.12: 203 8.12 - 12.17: 29 12.17 - 16.23: 2 16.23 - 20.29: 1 Bond angle restraints: 55706 Sorted by residual: angle pdb=" N1 C 5 23 " pdb=" C2 C 5 23 " pdb=" O2 C 5 23 " ideal model delta sigma weight residual 118.90 123.86 -4.96 6.00e-01 2.78e+00 6.84e+01 angle pdb=" O4' G 5 57 " pdb=" C1' G 5 57 " pdb=" N9 G 5 57 " ideal model delta sigma weight residual 108.20 114.43 -6.23 8.00e-01 1.56e+00 6.06e+01 angle pdb=" N PHE C 145 " pdb=" CA PHE C 145 " pdb=" C PHE C 145 " ideal model delta sigma weight residual 110.97 102.52 8.45 1.09e+00 8.42e-01 6.02e+01 angle pdb=" C1' C 5 23 " pdb=" N1 C 5 23 " pdb=" C2 C 5 23 " ideal model delta sigma weight residual 118.80 126.84 -8.04 1.10e+00 8.26e-01 5.34e+01 angle pdb=" O2 C 5 23 " pdb=" C2 C 5 23 " pdb=" N3 C 5 23 " ideal model delta sigma weight residual 121.90 116.96 4.94 7.00e-01 2.04e+00 4.99e+01 ... (remaining 55701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 20306 35.64 - 71.28: 723 71.28 - 106.92: 71 106.92 - 142.56: 3 142.56 - 178.20: 7 Dihedral angle restraints: 21110 sinusoidal: 7724 harmonic: 13386 Sorted by residual: dihedral pdb=" O4' C 5 38 " pdb=" C1' C 5 38 " pdb=" N1 C 5 38 " pdb=" C2 C 5 38 " ideal model delta sinusoidal sigma weight residual -128.00 46.85 -174.85 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C 5 71 " pdb=" C1' C 5 71 " pdb=" N1 C 5 71 " pdb=" C2 C 5 71 " ideal model delta sinusoidal sigma weight residual 232.00 76.66 155.34 1 1.70e+01 3.46e-03 6.34e+01 dihedral pdb=" O4' U 5 22 " pdb=" C1' U 5 22 " pdb=" N1 U 5 22 " pdb=" C2 U 5 22 " ideal model delta sinusoidal sigma weight residual 232.00 81.55 150.45 1 1.70e+01 3.46e-03 6.21e+01 ... (remaining 21107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3869 0.061 - 0.121: 761 0.121 - 0.182: 147 0.182 - 0.243: 4 0.243 - 0.303: 2 Chirality restraints: 4783 Sorted by residual: chirality pdb=" CG LEU A 950 " pdb=" CB LEU A 950 " pdb=" CD1 LEU A 950 " pdb=" CD2 LEU A 950 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C3' GTP C1001 " pdb=" C2' GTP C1001 " pdb=" C4' GTP C1001 " pdb=" O3' GTP C1001 " both_signs ideal model delta sigma weight residual False -2.47 -2.74 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C3' U 5 58 " pdb=" C4' U 5 58 " pdb=" O3' U 5 58 " pdb=" C2' U 5 58 " both_signs ideal model delta sigma weight residual False -2.48 -2.24 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 4780 not shown) Planarity restraints: 7833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G 5 57 " -0.069 2.00e-02 2.50e+03 3.12e-02 2.92e+01 pdb=" N9 G 5 57 " 0.077 2.00e-02 2.50e+03 pdb=" C8 G 5 57 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G 5 57 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G 5 57 " -0.000 2.00e-02 2.50e+03 pdb=" C6 G 5 57 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G 5 57 " -0.022 2.00e-02 2.50e+03 pdb=" N1 G 5 57 " -0.008 2.00e-02 2.50e+03 pdb=" C2 G 5 57 " 0.012 2.00e-02 2.50e+03 pdb=" N2 G 5 57 " -0.008 2.00e-02 2.50e+03 pdb=" N3 G 5 57 " 0.010 2.00e-02 2.50e+03 pdb=" C4 G 5 57 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 926 " -0.074 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO C 927 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO C 927 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 927 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 821 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ARG A 821 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG A 821 " -0.022 2.00e-02 2.50e+03 pdb=" N PHE A 822 " -0.019 2.00e-02 2.50e+03 ... (remaining 7830 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 563 2.64 - 3.21: 36485 3.21 - 3.77: 60389 3.77 - 4.34: 80946 4.34 - 4.90: 128837 Nonbonded interactions: 307220 Sorted by model distance: nonbonded pdb=" O LEU A1536 " pdb=" OG SER A1539 " model vdw 2.075 3.040 nonbonded pdb=" OD1 ASP A 200 " pdb=" NH2 ARG A 240 " model vdw 2.086 3.120 nonbonded pdb=" O LEU C 887 " pdb=" OG1 THR C 891 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR A1660 " pdb=" O ASN A1717 " model vdw 2.124 3.040 nonbonded pdb=" O PRO C 473 " pdb=" OG SER C 498 " model vdw 2.126 3.040 ... (remaining 307215 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.470 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: 0.030 Extract box with map and model: 0.740 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 47.740 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 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 : 0.005 0.080 41500 Z= 0.232 Angle : 0.761 20.290 55708 Z= 0.462 Chirality : 0.050 0.303 4783 Planarity : 0.005 0.108 7833 Dihedral : 16.756 178.198 14219 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 3.47 % Allowed : 24.38 % Favored : 72.15 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.11), residues: 6346 helix: 0.72 (0.10), residues: 2483 sheet: -0.64 (0.16), residues: 1049 loop : -0.85 (0.12), residues: 2814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 781 TYR 0.020 0.002 TYR C 537 PHE 0.032 0.002 PHE A1311 TRP 0.045 0.002 TRP A1668 HIS 0.009 0.001 HIS C 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.23 (41499) covalent geometry : angle 0.75901 / 0.46 (55706) SS BOND : bond 0.03778 / 1.99 ( 1) SS BOND : angle 8.65522 / 4.98 ( 2) hydrogen bonds : bond 0.18377 / 12.41 ( 2361) hydrogen bonds : angle 7.20525 / 5.03 ( 6709) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 361 time to evaluate : 0.937 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: A 453 TYR cc_start: 0.8381 (m-80) cc_final: 0.8147 (m-80) REVERT: A 1560 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7502 (tt) REVERT: C 397 ASP cc_start: 0.8218 (t0) cc_final: 0.7870 (t0) REVERT: C 668 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6683 (pm20) outliers start: 90 outliers final: 76 residues processed: 439 average time/residue: 0.2084 time to fit residues: 154.8309 Evaluate side-chains 420 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 342 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 208 GLN Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1194 CYS Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1440 THR Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1539 SER Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1574 ILE Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 735 PHE Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 944 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 50.0000 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 30.0000 chunk 523 optimal weight: 30.0000 chunk 497 optimal weight: 50.0000 chunk 414 optimal weight: 40.0000 chunk 310 optimal weight: 50.0000 chunk 488 optimal weight: 50.0000 chunk 366 optimal weight: 0.5980 chunk 597 optimal weight: 0.9990 overall best weight: 10.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 HIS ** A 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 994 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1026 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1121 ASN A1182 ASN A1188 ASN ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 GLN ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1466 ASN A2089 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.228649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.205879 restraints weight = 105414.588| |-----------------------------------------------------------------------------| r_work (start): 0.4468 rms_B_bonded: 2.20 r_work: 0.4130 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.4096 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4081 r_free = 0.4081 target_work(ls_wunit_k1) = 0.172 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.035 0.371 41500 Z= 1.428 Angle : 1.562 27.700 55708 Z= 0.801 Chirality : 0.119 1.104 4783 Planarity : 0.010 0.121 7833 Dihedral : 13.963 179.115 8425 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.50 % Favored : 94.33 % Rotamer: Outliers : 9.72 % Allowed : 20.37 % Favored : 69.91 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.10), residues: 6346 helix: -0.09 (0.10), residues: 2532 sheet: -0.80 (0.16), residues: 1083 loop : -1.25 (0.12), residues: 2731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.002 ARG C 645 TYR 0.058 0.007 TYR A 140 PHE 0.061 0.008 PHE A 128 TRP 0.082 0.008 TRP A 637 HIS 0.026 0.005 HIS C 890 Details of bonding type rmsd/Z covalent geometry : bond 0.03468 / 1.43 (41499) covalent geometry : angle 1.55769 / 0.80 (55706) SS BOND : bond 0.05148 / 2.71 ( 1) SS BOND : angle 18.91750 / 10.88 ( 2) hydrogen bonds : bond 0.08377 / 5.73 ( 2361) hydrogen bonds : angle 6.23552 / 4.37 ( 6709) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 252 poor density : 356 time to evaluate : 1.368 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: F 212 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6282 (mpp-170) REVERT: A 156 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8917 (ptt90) REVERT: A 251 ASP cc_start: 0.8855 (OUTLIER) cc_final: 0.8547 (m-30) REVERT: A 280 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: A 498 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7600 (ttp80) REVERT: A 641 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8195 (mtt) REVERT: A 981 PHE cc_start: 0.8968 (OUTLIER) cc_final: 0.8548 (m-10) REVERT: A 1216 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9239 (mt) REVERT: A 1249 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6480 (ttt) REVERT: A 1327 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8077 (mtm) REVERT: A 1341 ARG cc_start: 0.5910 (OUTLIER) cc_final: 0.4458 (tmm-80) REVERT: A 1450 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.6050 (tm-30) REVERT: A 1544 ARG cc_start: 0.7234 (ttm110) cc_final: 0.7002 (ptp90) REVERT: A 1734 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5487 (mpp) REVERT: A 2261 MET cc_start: 0.0110 (mpp) cc_final: -0.1348 (mpp) REVERT: C 174 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8546 (mt-10) REVERT: C 338 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8458 (mp0) REVERT: C 436 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: C 733 TRP cc_start: 0.8577 (OUTLIER) cc_final: 0.8274 (m-10) REVERT: C 790 LYS cc_start: 0.7552 (OUTLIER) cc_final: 0.7212 (mtpt) REVERT: C 892 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8432 (mt0) REVERT: C 943 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8836 (mt) outliers start: 252 outliers final: 148 residues processed: 561 average time/residue: 0.2166 time to fit residues: 201.9423 Evaluate side-chains 510 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 342 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 498 ARG Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 801 ILE Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 906 VAL Chi-restraints excluded: chain A residue 917 ILE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1024 HIS Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1176 SER Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1194 CYS Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1271 MET Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1303 LEU Chi-restraints excluded: chain A residue 1327 MET Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1382 SER Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1419 ILE Chi-restraints excluded: chain A residue 1440 THR Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1471 ARG Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 1734 MET Chi-restraints excluded: chain A residue 1735 LYS Chi-restraints excluded: chain D residue 251 LYS Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 261 ASP Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 355 LYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 358 LYS Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 397 ASP Chi-restraints excluded: chain C residue 405 LYS Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain C residue 436 GLN Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 532 ILE Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 581 LYS Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 759 LEU Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 892 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Chi-restraints excluded: chain C residue 944 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 280 optimal weight: 0.3980 chunk 158 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 176 optimal weight: 0.9980 chunk 520 optimal weight: 0.4980 chunk 314 optimal weight: 30.0000 chunk 145 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 604 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 238 optimal weight: 50.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS A 321 ASN A 333 HIS ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 994 ASN ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1460 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1615 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4786 r_free = 0.4786 target = 0.236829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.212724 restraints weight = 115659.850| |-----------------------------------------------------------------------------| r_work (start): 0.4544 rms_B_bonded: 2.77 r_work: 0.4193 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work: 0.4149 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4141 r_free = 0.4141 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4141 r_free = 0.4141 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 41500 Z= 0.175 Angle : 0.654 15.030 55708 Z= 0.344 Chirality : 0.047 0.323 4783 Planarity : 0.005 0.107 7833 Dihedral : 13.487 177.725 8396 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % Rotamer: Outliers : 4.94 % Allowed : 22.84 % Favored : 72.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.11), residues: 6346 helix: 0.89 (0.10), residues: 2504 sheet: -0.67 (0.16), residues: 1053 loop : -0.93 (0.12), residues: 2789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A1427 TYR 0.024 0.002 TYR A1671 PHE 0.026 0.002 PHE A 827 TRP 0.029 0.002 TRP A 637 HIS 0.009 0.001 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (41499) covalent geometry : angle 0.65118 / 0.34 (55706) SS BOND : bond 0.03513 / 1.85 ( 1) SS BOND : angle 10.48020 / 6.04 ( 2) hydrogen bonds : bond 0.04260 / 2.92 ( 2361) hydrogen bonds : angle 4.93665 / 3.45 ( 6709) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 362 time to evaluate : 1.369 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 156 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8751 (ttp-170) REVERT: A 227 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.8424 (mtm110) REVERT: A 297 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8434 (p0) REVERT: A 980 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7331 (tpt170) REVERT: A 981 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8020 (m-10) REVERT: A 1327 MET cc_start: 0.8219 (mtm) cc_final: 0.7883 (mtm) REVERT: A 2261 MET cc_start: 0.0242 (mpp) cc_final: -0.0984 (mpp) REVERT: A 2284 MET cc_start: -0.2405 (pp-130) cc_final: -0.3408 (pp-130) REVERT: C 521 ASP cc_start: 0.8214 (t0) cc_final: 0.7833 (t0) REVERT: C 790 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7072 (mtpt) REVERT: C 827 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8593 (tp) REVERT: C 856 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.7784 (p-80) REVERT: C 892 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8438 (mt0) REVERT: C 943 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8789 (mt) outliers start: 128 outliers final: 86 residues processed: 474 average time/residue: 0.2150 time to fit residues: 171.4276 Evaluate side-chains 439 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 343 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 210 HIS Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 321 ASN Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 980 ARG Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1297 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1448 LEU Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1574 ILE Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1639 VAL Chi-restraints excluded: chain A residue 1667 ARG Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 495 ARG Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 892 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 123 optimal weight: 0.6980 chunk 185 optimal weight: 20.0000 chunk 474 optimal weight: 9.9990 chunk 32 optimal weight: 0.0020 chunk 623 optimal weight: 0.0020 chunk 150 optimal weight: 0.9990 chunk 310 optimal weight: 40.0000 chunk 43 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 563 optimal weight: 0.7980 chunk 94 optimal weight: 7.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS A 321 ASN ** A 904 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 GLN ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1460 HIS A1554 GLN ** C 924 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.237194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.211908 restraints weight = 136620.243| |-----------------------------------------------------------------------------| r_work (start): 0.4533 rms_B_bonded: 2.24 r_work: 0.4244 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.4191 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4186 r_free = 0.4186 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4186 r_free = 0.4186 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 41500 Z= 0.143 Angle : 0.580 14.346 55708 Z= 0.303 Chirality : 0.045 0.373 4783 Planarity : 0.004 0.072 7833 Dihedral : 13.233 179.955 8381 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.01 % Rotamer: Outliers : 4.48 % Allowed : 22.45 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.11), residues: 6346 helix: 1.34 (0.11), residues: 2523 sheet: -0.58 (0.16), residues: 1061 loop : -0.73 (0.12), residues: 2762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 845 TYR 0.016 0.002 TYR A1620 PHE 0.023 0.002 PHE A1099 TRP 0.044 0.002 TRP A1661 HIS 0.008 0.001 HIS A 210 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (41499) covalent geometry : angle 0.57661 / 0.30 (55706) SS BOND : bond 0.03522 / 1.85 ( 1) SS BOND : angle 9.99975 / 5.75 ( 2) hydrogen bonds : bond 0.03656 / 2.50 ( 2361) hydrogen bonds : angle 4.50443 / 3.15 ( 6709) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 358 time to evaluate : 1.317 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 227 ARG cc_start: 0.8600 (OUTLIER) cc_final: 0.8365 (mtm110) REVERT: A 297 ASN cc_start: 0.8933 (OUTLIER) cc_final: 0.8640 (p0) REVERT: A 474 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7664 (mtt90) REVERT: A 899 MET cc_start: 0.5652 (OUTLIER) cc_final: 0.5326 (mmt) REVERT: A 981 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8049 (m-10) REVERT: A 2261 MET cc_start: 0.0279 (mpp) cc_final: -0.0758 (mpp) REVERT: A 2284 MET cc_start: -0.2606 (pp-130) cc_final: -0.3285 (pp-130) REVERT: C 236 MET cc_start: 0.8676 (mmp) cc_final: 0.8324 (mmt) REVERT: C 397 ASP cc_start: 0.8169 (t0) cc_final: 0.7733 (t0) REVERT: C 668 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6577 (pt0) REVERT: C 692 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8024 (mp) REVERT: C 790 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7249 (mtpt) REVERT: C 856 HIS cc_start: 0.8167 (OUTLIER) cc_final: 0.7779 (p-80) REVERT: C 943 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8768 (mt) outliers start: 116 outliers final: 74 residues processed: 456 average time/residue: 0.2324 time to fit residues: 178.1713 Evaluate side-chains 427 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 343 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 899 MET Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1335 ILE Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1438 VAL Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1554 GLN Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1652 MET Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1667 ARG Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 377 TYR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 212 optimal weight: 50.0000 chunk 474 optimal weight: 9.9990 chunk 149 optimal weight: 0.7980 chunk 461 optimal weight: 40.0000 chunk 454 optimal weight: 50.0000 chunk 438 optimal weight: 30.0000 chunk 482 optimal weight: 10.0000 chunk 388 optimal weight: 0.3980 chunk 467 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 330 optimal weight: 50.0000 overall best weight: 4.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 GLN ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 GLN ** A1363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1554 GLN ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.232610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.207415 restraints weight = 128559.790| |-----------------------------------------------------------------------------| r_work (start): 0.4483 rms_B_bonded: 2.11 r_work: 0.4203 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4162 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4153 r_free = 0.4153 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4153 r_free = 0.4153 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6783 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.191 41500 Z= 0.704 Angle : 0.957 19.478 55708 Z= 0.489 Chirality : 0.071 0.674 4783 Planarity : 0.006 0.085 7833 Dihedral : 13.368 179.646 8361 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 6.02 % Allowed : 22.45 % Favored : 71.53 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.11), residues: 6346 helix: 1.08 (0.11), residues: 2517 sheet: -0.56 (0.16), residues: 1104 loop : -0.93 (0.12), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 339 TYR 0.038 0.004 TYR A 431 PHE 0.040 0.004 PHE A1099 TRP 0.050 0.005 TRP A 637 HIS 0.015 0.003 HIS C 928 Details of bonding type rmsd/Z covalent geometry : bond 0.01714 / 0.70 (41499) covalent geometry : angle 0.95209 / 0.49 (55706) SS BOND : bond 0.04754 / 2.50 ( 1) SS BOND : angle 15.80414 / 9.07 ( 2) hydrogen bonds : bond 0.05405 / 3.72 ( 2361) hydrogen bonds : angle 4.87356 / 3.41 ( 6709) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 351 time to evaluate : 1.497 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: F 177 ARG cc_start: 0.6754 (OUTLIER) cc_final: 0.6191 (ppp80) REVERT: F 208 GLN cc_start: 0.6754 (pm20) cc_final: 0.6323 (pm20) REVERT: F 212 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6303 (mpp-170) REVERT: A 156 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.8867 (ptt90) REVERT: A 280 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: A 297 ASN cc_start: 0.8990 (OUTLIER) cc_final: 0.8704 (p0) REVERT: A 334 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8606 (m) REVERT: A 641 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7804 (mtp) REVERT: A 980 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7510 (tpt170) REVERT: A 981 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.8326 (m-10) REVERT: A 1450 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.5934 (tm-30) REVERT: A 2261 MET cc_start: 0.0271 (mpp) cc_final: -0.0665 (mpp) REVERT: A 2284 MET cc_start: -0.2429 (OUTLIER) cc_final: -0.2999 (pp-130) REVERT: E 155 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5827 (pm20) REVERT: D 324 MET cc_start: 0.7866 (mmp) cc_final: 0.7632 (mmp) REVERT: C 236 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8527 (mmp) REVERT: C 338 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: C 418 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9063 (tp) REVERT: C 892 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8439 (mt0) REVERT: C 943 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8857 (mt) outliers start: 156 outliers final: 106 residues processed: 480 average time/residue: 0.2460 time to fit residues: 198.5689 Evaluate side-chains 464 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 341 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 221 ASN Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 271 MET Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 980 ARG Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1194 CYS Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1630 LEU Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1659 LYS Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 892 GLN Chi-restraints excluded: chain C residue 906 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 64 optimal weight: 0.5980 chunk 553 optimal weight: 50.0000 chunk 98 optimal weight: 0.9980 chunk 345 optimal weight: 50.0000 chunk 288 optimal weight: 40.0000 chunk 554 optimal weight: 9.9990 chunk 396 optimal weight: 7.9990 chunk 558 optimal weight: 40.0000 chunk 199 optimal weight: 50.0000 chunk 449 optimal weight: 40.0000 chunk 395 optimal weight: 10.0000 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1363 GLN ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1466 ASN ** A1658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.231479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.210292 restraints weight = 130761.551| |-----------------------------------------------------------------------------| r_work (start): 0.4517 rms_B_bonded: 1.63 r_work: 0.4220 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.4183 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.4183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4169 r_free = 0.4169 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 18 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4169 r_free = 0.4169 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.216 41500 Z= 0.840 Angle : 1.079 20.077 55708 Z= 0.552 Chirality : 0.079 0.806 4783 Planarity : 0.007 0.109 7833 Dihedral : 13.459 179.973 8354 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 8.22 % Allowed : 21.41 % Favored : 70.37 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.32 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.11), residues: 6346 helix: 0.82 (0.11), residues: 2521 sheet: -0.64 (0.16), residues: 1126 loop : -1.02 (0.12), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG A1427 TYR 0.048 0.004 TYR A1671 PHE 0.041 0.005 PHE C 331 TRP 0.057 0.005 TRP A 637 HIS 0.022 0.003 HIS C 928 Details of bonding type rmsd/Z covalent geometry : bond 0.02042 / 0.84 (41499) covalent geometry : angle 1.07410 / 0.55 (55706) SS BOND : bond 0.04798 / 2.53 ( 1) SS BOND : angle 16.47207 / 9.42 ( 2) hydrogen bonds : bond 0.05960 / 4.12 ( 2361) hydrogen bonds : angle 5.03770 / 3.53 ( 6709) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 350 time to evaluate : 1.502 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: F 177 ARG cc_start: 0.6844 (OUTLIER) cc_final: 0.6315 (ppp80) REVERT: F 208 GLN cc_start: 0.6850 (pm20) cc_final: 0.6593 (pm20) REVERT: F 212 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6294 (mpp-170) REVERT: A 156 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8821 (ptt90) REVERT: A 251 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8612 (m-30) REVERT: A 334 THR cc_start: 0.8899 (OUTLIER) cc_final: 0.8638 (m) REVERT: A 474 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7824 (mtt90) REVERT: A 641 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7821 (mtp) REVERT: A 980 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7640 (tpt170) REVERT: A 981 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.8341 (m-10) REVERT: A 1249 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.6302 (ttt) REVERT: A 1341 ARG cc_start: 0.5848 (OUTLIER) cc_final: 0.5070 (tmm-80) REVERT: A 1450 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6202 (tm-30) REVERT: A 1576 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8185 (tp) REVERT: A 2261 MET cc_start: 0.0379 (mpp) cc_final: -0.0528 (mpp) REVERT: A 2284 MET cc_start: -0.2556 (OUTLIER) cc_final: -0.3054 (pp-130) REVERT: E 155 GLU cc_start: 0.5847 (OUTLIER) cc_final: 0.5522 (pm20) REVERT: C 147 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8056 (m-30) REVERT: C 174 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8522 (mt-10) REVERT: C 338 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: C 418 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9053 (tp) REVERT: C 733 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7769 (m-10) REVERT: C 892 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8443 (mt0) REVERT: C 943 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8880 (mt) outliers start: 213 outliers final: 141 residues processed: 526 average time/residue: 0.2423 time to fit residues: 213.7564 Evaluate side-chains 505 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 342 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain F residue 195 SER Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain F residue 212 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 111 GLU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 301 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 387 PHE Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 550 VAL Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 793 ASN Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 904 HIS Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 952 VAL Chi-restraints excluded: chain A residue 965 VAL Chi-restraints excluded: chain A residue 980 ARG Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1038 SER Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1194 CYS Chi-restraints excluded: chain A residue 1211 ASP Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1259 ILE Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1391 LEU Chi-restraints excluded: chain A residue 1419 ILE Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1456 THR Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1464 LEU Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1576 ILE Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1710 ASN Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain E residue 108 LEU Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 236 MET Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 299 ILE Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 452 THR Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 559 ILE Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 733 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 749 THR Chi-restraints excluded: chain C residue 767 VAL Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 892 GLN Chi-restraints excluded: chain C residue 906 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 910 ASP Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 290 optimal weight: 50.0000 chunk 271 optimal weight: 40.0000 chunk 255 optimal weight: 0.4980 chunk 391 optimal weight: 50.0000 chunk 147 optimal weight: 0.6980 chunk 626 optimal weight: 0.7980 chunk 242 optimal weight: 30.0000 chunk 397 optimal weight: 9.9990 chunk 498 optimal weight: 30.0000 chunk 138 optimal weight: 7.9990 chunk 178 optimal weight: 0.0980 overall best weight: 2.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 GLN ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1363 GLN ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1466 ASN A1658 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4771 r_free = 0.4771 target = 0.235177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.213988 restraints weight = 130042.309| |-----------------------------------------------------------------------------| r_work (start): 0.4549 rms_B_bonded: 1.67 r_work: 0.4252 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4216 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4206 r_free = 0.4206 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4206 r_free = 0.4206 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.4206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.149 41500 Z= 0.326 Angle : 0.713 17.303 55708 Z= 0.368 Chirality : 0.051 0.393 4783 Planarity : 0.005 0.107 7833 Dihedral : 13.293 178.366 8350 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % Rotamer: Outliers : 5.05 % Allowed : 25.08 % Favored : 69.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.11), residues: 6346 helix: 1.23 (0.11), residues: 2522 sheet: -0.52 (0.16), residues: 1105 loop : -0.86 (0.12), residues: 2719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1427 TYR 0.033 0.002 TYR A1671 PHE 0.033 0.003 PHE A 411 TRP 0.043 0.003 TRP A1668 HIS 0.011 0.002 HIS C 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.33 (41499) covalent geometry : angle 0.70882 / 0.37 (55706) SS BOND : bond 0.04018 / 2.11 ( 1) SS BOND : angle 12.28610 / 7.03 ( 2) hydrogen bonds : bond 0.04269 / 2.95 ( 2361) hydrogen bonds : angle 4.52814 / 3.17 ( 6709) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 355 time to evaluate : 1.634 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: F 177 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.6196 (ppp80) REVERT: A 297 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8464 (p0) REVERT: A 334 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8514 (m) REVERT: A 474 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7637 (mtt90) REVERT: A 641 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7405 (mtp) REVERT: A 980 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7351 (tpt170) REVERT: A 981 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.8059 (m-10) REVERT: A 1341 ARG cc_start: 0.5731 (OUTLIER) cc_final: 0.4994 (tmm-80) REVERT: A 1450 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6125 (tm-30) REVERT: A 1576 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8054 (tp) REVERT: A 2261 MET cc_start: 0.0263 (mpp) cc_final: -0.0501 (mpp) REVERT: A 2284 MET cc_start: -0.2674 (OUTLIER) cc_final: -0.3135 (pp-130) REVERT: E 155 GLU cc_start: 0.5856 (OUTLIER) cc_final: 0.5618 (pm20) REVERT: C 147 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7786 (m-30) REVERT: C 174 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8446 (mt-10) REVERT: C 394 ARG cc_start: 0.7837 (ttp80) cc_final: 0.7469 (mtm-85) REVERT: C 856 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.7903 (p-80) REVERT: C 943 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8842 (mt) outliers start: 131 outliers final: 95 residues processed: 459 average time/residue: 0.2474 time to fit residues: 190.1108 Evaluate side-chains 458 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 347 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 177 ARG Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 980 ARG Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1194 CYS Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1466 ASN Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1576 ILE Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1659 LYS Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 495 ARG Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 905 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 93 optimal weight: 7.9990 chunk 525 optimal weight: 7.9990 chunk 496 optimal weight: 30.0000 chunk 38 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 498 optimal weight: 10.0000 chunk 308 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 360 optimal weight: 50.0000 chunk 397 optimal weight: 0.4980 chunk 359 optimal weight: 8.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1615 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.234573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.209687 restraints weight = 125984.600| |-----------------------------------------------------------------------------| r_work (start): 0.4508 rms_B_bonded: 2.35 r_work: 0.4205 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.4168 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4160 r_free = 0.4160 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.161 41500 Z= 0.383 Angle : 0.743 17.741 55708 Z= 0.382 Chirality : 0.054 0.457 4783 Planarity : 0.005 0.095 7833 Dihedral : 13.253 179.018 8350 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.02 % Favored : 95.94 % Rotamer: Outliers : 5.90 % Allowed : 24.15 % Favored : 69.95 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.11), residues: 6346 helix: 1.32 (0.11), residues: 2524 sheet: -0.48 (0.16), residues: 1128 loop : -0.81 (0.12), residues: 2694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1427 TYR 0.033 0.002 TYR A1671 PHE 0.035 0.003 PHE A 411 TRP 0.039 0.003 TRP A 651 HIS 0.013 0.002 HIS C 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00933 / 0.38 (41499) covalent geometry : angle 0.73877 / 0.38 (55706) SS BOND : bond 0.04401 / 2.32 ( 1) SS BOND : angle 13.18191 / 7.55 ( 2) hydrogen bonds : bond 0.04347 / 3.00 ( 2361) hydrogen bonds : angle 4.49107 / 3.15 ( 6709) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 349 time to evaluate : 1.489 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 61 MET cc_start: 0.8084 (mtp) cc_final: 0.7711 (mmm) REVERT: A 251 ASP cc_start: 0.8821 (OUTLIER) cc_final: 0.8577 (m-30) REVERT: A 297 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8503 (p0) REVERT: A 334 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8653 (m) REVERT: A 474 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7723 (mtt90) REVERT: A 641 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7684 (mtp) REVERT: A 980 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7383 (tpt170) REVERT: A 981 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.8129 (m-10) REVERT: A 1249 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.6252 (ttt) REVERT: A 1341 ARG cc_start: 0.5790 (OUTLIER) cc_final: 0.5212 (tmm-80) REVERT: A 1450 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6141 (tm-30) REVERT: A 1576 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.8004 (tp) REVERT: A 2261 MET cc_start: 0.0378 (mpp) cc_final: -0.0288 (mpp) REVERT: A 2284 MET cc_start: -0.2870 (OUTLIER) cc_final: -0.3324 (pp-130) REVERT: E 155 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5667 (pm20) REVERT: C 147 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7879 (m-30) REVERT: C 174 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8449 (mt-10) REVERT: C 236 MET cc_start: 0.8728 (mmp) cc_final: 0.8394 (mmp) REVERT: C 628 VAL cc_start: 0.9229 (OUTLIER) cc_final: 0.8930 (t) REVERT: C 692 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8073 (mp) REVERT: C 856 HIS cc_start: 0.8254 (OUTLIER) cc_final: 0.7926 (p-80) REVERT: C 943 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8842 (mt) outliers start: 153 outliers final: 114 residues processed: 478 average time/residue: 0.2146 time to fit residues: 173.0037 Evaluate side-chains 481 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 348 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 266 SER Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 641 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 904 HIS Chi-restraints excluded: chain A residue 914 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 980 ARG Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1165 VAL Chi-restraints excluded: chain A residue 1180 LYS Chi-restraints excluded: chain A residue 1184 ASN Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1194 CYS Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1257 THR Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1341 ARG Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1450 GLN Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1576 ILE Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1659 LYS Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 174 GLU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 197 SER Chi-restraints excluded: chain C residue 243 ILE Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 352 LYS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 440 SER Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 495 ARG Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 848 THR Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 889 THR Chi-restraints excluded: chain C residue 905 GLN Chi-restraints excluded: chain C residue 906 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 917 VAL Chi-restraints excluded: chain C residue 918 ILE Chi-restraints excluded: chain C residue 943 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 193 optimal weight: 30.0000 chunk 47 optimal weight: 0.1980 chunk 375 optimal weight: 20.0000 chunk 257 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 335 optimal weight: 3.9990 chunk 331 optimal weight: 40.0000 chunk 98 optimal weight: 0.0970 chunk 634 optimal weight: 0.5980 chunk 563 optimal weight: 0.6980 chunk 494 optimal weight: 20.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS A 834 HIS A1111 GLN ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1363 GLN A1458 GLN A1638 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4795 r_free = 0.4795 target = 0.237577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.212211 restraints weight = 124328.139| |-----------------------------------------------------------------------------| r_work (start): 0.4532 rms_B_bonded: 2.14 r_work: 0.4258 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.4221 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.4221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4213 r_free = 0.4213 target_work(ls_wunit_k1) = 0.183 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 41500 Z= 0.145 Angle : 0.603 15.513 55708 Z= 0.313 Chirality : 0.045 0.333 4783 Planarity : 0.004 0.085 7833 Dihedral : 13.079 179.959 8350 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.06 % Rotamer: Outliers : 3.74 % Allowed : 26.27 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.11), residues: 6346 helix: 1.57 (0.11), residues: 2538 sheet: -0.31 (0.16), residues: 1065 loop : -0.64 (0.12), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 355 TYR 0.027 0.002 TYR A1671 PHE 0.024 0.002 PHE A 827 TRP 0.031 0.002 TRP A1668 HIS 0.007 0.001 HIS C 928 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 (41499) covalent geometry : angle 0.60022 / 0.31 (55706) SS BOND : bond 0.03459 / 1.82 ( 1) SS BOND : angle 9.61985 / 5.48 ( 2) hydrogen bonds : bond 0.03480 / 2.40 ( 2361) hydrogen bonds : angle 4.17377 / 2.92 ( 6709) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 356 time to evaluate : 1.627 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 297 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8512 (p0) REVERT: A 334 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8534 (m) REVERT: A 980 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7201 (tpt170) REVERT: A 981 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.7895 (m-10) REVERT: A 1119 ASP cc_start: 0.6171 (p0) cc_final: 0.5956 (p0) REVERT: A 1560 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7586 (tt) REVERT: A 2261 MET cc_start: 0.0336 (mpp) cc_final: -0.0250 (mpp) REVERT: A 2284 MET cc_start: -0.2735 (OUTLIER) cc_final: -0.3199 (pp-130) REVERT: C 236 MET cc_start: 0.8655 (mmp) cc_final: 0.8352 (mmt) REVERT: C 397 ASP cc_start: 0.8172 (t0) cc_final: 0.7834 (t70) REVERT: C 668 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6577 (pt0) REVERT: C 692 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8107 (mp) REVERT: C 856 HIS cc_start: 0.8139 (OUTLIER) cc_final: 0.7677 (p-80) REVERT: C 943 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8779 (mt) outliers start: 97 outliers final: 75 residues processed: 433 average time/residue: 0.2408 time to fit residues: 176.5904 Evaluate side-chains 431 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 346 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 122 ASN Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 980 ARG Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1032 ARG Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1427 ARG Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1659 LYS Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 311 SER Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 495 ARG Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 943 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 336 optimal weight: 0.0060 chunk 40 optimal weight: 0.6980 chunk 509 optimal weight: 50.0000 chunk 230 optimal weight: 10.0000 chunk 580 optimal weight: 0.5980 chunk 529 optimal weight: 50.0000 chunk 257 optimal weight: 3.9990 chunk 474 optimal weight: 8.9990 chunk 550 optimal weight: 50.0000 chunk 157 optimal weight: 8.9990 chunk 245 optimal weight: 50.0000 overall best weight: 2.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 HIS ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.234362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.210783 restraints weight = 112777.644| |-----------------------------------------------------------------------------| r_work (start): 0.4521 rms_B_bonded: 2.64 r_work: 0.4190 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work: 0.4146 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4139 r_free = 0.4139 target_work(ls_wunit_k1) = 0.177 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.4139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.164 41500 Z= 0.435 Angle : 0.770 17.818 55708 Z= 0.394 Chirality : 0.056 0.494 4783 Planarity : 0.005 0.073 7833 Dihedral : 13.119 179.687 8343 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.08 % Rotamer: Outliers : 3.90 % Allowed : 26.23 % Favored : 69.87 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.11), residues: 6346 helix: 1.44 (0.11), residues: 2542 sheet: -0.35 (0.16), residues: 1116 loop : -0.67 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 222 TYR 0.034 0.003 TYR A1671 PHE 0.036 0.003 PHE A 411 TRP 0.040 0.003 TRP A 651 HIS 0.013 0.002 HIS C 928 Details of bonding type rmsd/Z covalent geometry : bond 0.01063 / 0.43 (41499) covalent geometry : angle 0.76580 / 0.39 (55706) SS BOND : bond 0.04461 / 2.35 ( 1) SS BOND : angle 13.54144 / 7.76 ( 2) hydrogen bonds : bond 0.04361 / 3.00 ( 2361) hydrogen bonds : angle 4.37379 / 3.06 ( 6709) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12692 Ramachandran restraints generated. 6346 Oldfield, 0 Emsley, 6346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 350 time to evaluate : 1.582 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 251 ASP cc_start: 0.8920 (OUTLIER) cc_final: 0.8445 (m-30) REVERT: A 297 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8574 (p0) REVERT: A 334 THR cc_start: 0.8949 (OUTLIER) cc_final: 0.8694 (m) REVERT: A 980 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7376 (tpt170) REVERT: A 981 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8120 (m-10) REVERT: A 1249 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.6243 (ttt) REVERT: A 1560 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7524 (tt) REVERT: A 2261 MET cc_start: 0.0410 (mpp) cc_final: -0.0119 (mpp) REVERT: A 2284 MET cc_start: -0.2773 (OUTLIER) cc_final: -0.3214 (pp-130) REVERT: C 236 MET cc_start: 0.8787 (mmp) cc_final: 0.8427 (mmp) REVERT: C 397 ASP cc_start: 0.8230 (t0) cc_final: 0.7781 (t0) REVERT: C 628 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8916 (t) REVERT: C 668 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6887 (pt0) REVERT: C 692 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8023 (mp) REVERT: C 856 HIS cc_start: 0.8235 (OUTLIER) cc_final: 0.7893 (p-80) REVERT: C 943 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8830 (mt) outliers start: 101 outliers final: 84 residues processed: 437 average time/residue: 0.2423 time to fit residues: 179.4641 Evaluate side-chains 445 residues out of total 5702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 348 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 297 ASN Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 374 ASP Chi-restraints excluded: chain A residue 506 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 593 ARG Chi-restraints excluded: chain A residue 598 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 980 ARG Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1009 MET Chi-restraints excluded: chain A residue 1023 ASN Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1089 CYS Chi-restraints excluded: chain A residue 1121 ASN Chi-restraints excluded: chain A residue 1193 GLU Chi-restraints excluded: chain A residue 1234 ASP Chi-restraints excluded: chain A residue 1244 VAL Chi-restraints excluded: chain A residue 1249 MET Chi-restraints excluded: chain A residue 1255 THR Chi-restraints excluded: chain A residue 1268 ILE Chi-restraints excluded: chain A residue 1301 ILE Chi-restraints excluded: chain A residue 1372 ILE Chi-restraints excluded: chain A residue 1385 VAL Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1482 GLU Chi-restraints excluded: chain A residue 1493 THR Chi-restraints excluded: chain A residue 1502 PHE Chi-restraints excluded: chain A residue 1549 VAL Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1560 ILE Chi-restraints excluded: chain A residue 1615 HIS Chi-restraints excluded: chain A residue 1656 THR Chi-restraints excluded: chain A residue 1659 LYS Chi-restraints excluded: chain A residue 2147 MET Chi-restraints excluded: chain A residue 2284 MET Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 280 GLU Chi-restraints excluded: chain D residue 282 THR Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 293 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 312 SER Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 353 THR Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 365 SER Chi-restraints excluded: chain C residue 388 VAL Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 495 ARG Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 581 LYS Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 628 VAL Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 668 GLU Chi-restraints excluded: chain C residue 669 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain C residue 770 PHE Chi-restraints excluded: chain C residue 790 LYS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain C residue 856 HIS Chi-restraints excluded: chain C residue 859 GLN Chi-restraints excluded: chain C residue 905 GLN Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 943 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 59 optimal weight: 1.9990 chunk 393 optimal weight: 30.0000 chunk 576 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 207 optimal weight: 40.0000 chunk 563 optimal weight: 0.5980 chunk 565 optimal weight: 0.9980 chunk 357 optimal weight: 8.9990 chunk 603 optimal weight: 0.0980 chunk 364 optimal weight: 9.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.237317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.212379 restraints weight = 122249.700| |-----------------------------------------------------------------------------| r_work (start): 0.4537 rms_B_bonded: 2.35 r_work: 0.4238 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.4193 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4184 r_free = 0.4184 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4184 r_free = 0.4184 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.4184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 41500 Z= 0.147 Angle : 0.611 15.863 55708 Z= 0.316 Chirality : 0.045 0.342 4783 Planarity : 0.004 0.059 7833 Dihedral : 12.996 179.731 8342 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.91 % Favored : 97.08 % Rotamer: Outliers : 3.59 % Allowed : 26.43 % Favored : 69.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.11), residues: 6346 helix: 1.65 (0.11), residues: 2541 sheet: -0.25 (0.16), residues: 1079 loop : -0.56 (0.12), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 222 TYR 0.028 0.002 TYR A1671 PHE 0.024 0.002 PHE A1088 TRP 0.029 0.002 TRP A 637 HIS 0.012 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (41499) covalent geometry : angle 0.60863 / 0.31 (55706) SS BOND : bond 0.03591 / 1.89 ( 1) SS BOND : angle 9.79368 / 5.59 ( 2) hydrogen bonds : bond 0.03466 / 2.38 ( 2361) hydrogen bonds : angle 4.10684 / 2.87 ( 6709) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13051.68 seconds wall clock time: 222 minutes 46.71 seconds (13366.71 seconds total)