Starting phenix.real_space_refine on Sat Mar 7 03:12:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7x29_32962/03_2026/7x29_32962_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7x29_32962/03_2026/7x29_32962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7x29_32962/03_2026/7x29_32962_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7x29_32962/03_2026/7x29_32962_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7x29_32962/03_2026/7x29_32962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7x29_32962/03_2026/7x29_32962.map" } resolution = 2.49 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5870 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 163 5.16 5 C 20536 2.51 5 N 5420 2.21 5 O 6334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 188 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32453 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 7657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 991, 7657 Classifications: {'peptide': 991} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 46, 'TRANS': 943} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 9186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9186 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 2, 'PTRANS': 59, 'TRANS': 1128} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 9186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1190, 9186 Classifications: {'peptide': 1190} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 3, 'PTRANS': 59, 'TRANS': 1127} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 1589 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1583 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 214, 1583 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1609 Chain: "G" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 221, 1627 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 208} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1655 Chain: "K" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1601 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 7.49, per 1000 atoms: 0.23 Number of scatterers: 32453 At special positions: 0 Unit cell: (152.632, 190.52, 240.315, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 163 16.00 O 6334 8.00 N 5420 7.00 C 20536 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.04 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.02 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.04 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.04 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.04 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.04 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.05 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.04 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 203 " distance=2.02 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.04 Simple disulfide: pdb=" SG CYS G 135 " - pdb=" SG CYS G 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 203 " distance=2.02 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 135 " - pdb=" SG CYS K 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.5 seconds 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7840 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 72 sheets defined 20.7% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.648A pdb=" N PHE A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.690A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 273 removed outlier: 4.059A pdb=" N LEU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 825 removed outlier: 3.763A pdb=" N LEU A 820 " --> pdb=" O LYS A 816 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 854 removed outlier: 4.056A pdb=" N SER A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 915 removed outlier: 3.668A pdb=" N GLN A 914 " --> pdb=" O ASP A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 931 removed outlier: 3.893A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 957 removed outlier: 4.045A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 984 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1012 removed outlier: 3.604A pdb=" N MET A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLN A1009 " --> pdb=" O LEU A1005 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE A1012 " --> pdb=" O MET A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1042 removed outlier: 3.600A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 3.913A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1223 Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.737A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.937A pdb=" N LEU B 273 " --> pdb=" O ARG B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 410 through 418 removed outlier: 3.554A pdb=" N LEU B 414 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE B 418 " --> pdb=" O LEU B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 435 removed outlier: 3.910A pdb=" N ALA B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER B 435 " --> pdb=" O ALA B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 removed outlier: 3.545A pdb=" N MET B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 814 through 825 removed outlier: 3.728A pdb=" N TYR B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 854 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 915 removed outlier: 3.753A pdb=" N GLN B 914 " --> pdb=" O ASP B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 931 removed outlier: 4.032A pdb=" N TYR B 928 " --> pdb=" O ILE B 924 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL B 929 " --> pdb=" O CYS B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 957 removed outlier: 3.997A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 984 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1010 removed outlier: 3.842A pdb=" N THR B1010 " --> pdb=" O GLY B1006 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1042 removed outlier: 3.716A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1106 removed outlier: 3.881A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.525A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.602A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 273 removed outlier: 3.997A pdb=" N LEU C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 385 through 390 Processing helix chain 'C' and resid 410 through 418 removed outlier: 3.681A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 435 removed outlier: 3.551A pdb=" N ALA C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER C 435 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 removed outlier: 3.823A pdb=" N SER C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.562A pdb=" N GLU C 823 " --> pdb=" O GLN C 819 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TYR C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 854 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 907 through 915 removed outlier: 3.760A pdb=" N GLN C 914 " --> pdb=" O ASP C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 931 removed outlier: 4.037A pdb=" N TYR C 928 " --> pdb=" O ILE C 924 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL C 929 " --> pdb=" O CYS C 925 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 957 removed outlier: 4.078A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 984 Processing helix chain 'C' and resid 986 through 993 Processing helix chain 'C' and resid 993 through 1012 removed outlier: 3.574A pdb=" N MET C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN C1009 " --> pdb=" O LEU C1005 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C1012 " --> pdb=" O MET C1008 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1042 removed outlier: 3.738A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 3.714A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 161 through 165 Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.503A pdb=" N SER G 84 " --> pdb=" O PRO G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 128 removed outlier: 4.066A pdb=" N LEU G 126 " --> pdb=" O SER G 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.513A pdb=" N SER K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 127 removed outlier: 3.641A pdb=" N LYS K 127 " --> pdb=" O GLU K 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 35 removed outlier: 7.099A pdb=" N HIS A 91 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.335A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY C 372 " --> pdb=" O CYS C 603 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 75 removed outlier: 4.261A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 5.936A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.280A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AA7, first strand: chain 'A' and resid 127 through 129 removed outlier: 3.840A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 187 through 189 Processing sheet with id=AA9, first strand: chain 'A' and resid 689 through 690 removed outlier: 4.470A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 372 through 376 removed outlier: 6.534A pdb=" N GLY A 372 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N SER A 607 " --> pdb=" O GLY A 372 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL A 374 " --> pdb=" O SER A 607 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 717 through 724 removed outlier: 6.834A pdb=" N MET A 757 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N SER A 720 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU A 759 " --> pdb=" O SER A 720 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N LEU A 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 732 " --> pdb=" O LEU A 735 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA A 737 " --> pdb=" O PRO A 730 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.634A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1121 through 1129 removed outlier: 5.921A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1121 through 1129 removed outlier: 5.921A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS A 779 " --> pdb=" O ALA B 969 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB7, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AB8, first strand: chain 'A' and resid 967 through 968 removed outlier: 7.005A pdb=" N LYS C 779 " --> pdb=" O VAL C1150 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1150 " --> pdb=" O LYS C 779 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER C 781 " --> pdb=" O GLU C1148 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU C1148 " --> pdb=" O SER C 781 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N HIS C1146 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C1124 " --> pdb=" O VAL C1139 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 967 through 968 removed outlier: 7.005A pdb=" N LYS C 779 " --> pdb=" O VAL C1150 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1150 " --> pdb=" O LYS C 779 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER C 781 " --> pdb=" O GLU C1148 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU C1148 " --> pdb=" O SER C 781 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N HIS C1146 " --> pdb=" O PRO C 783 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL C1150 " --> pdb=" O LYS C1174 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C1172 " --> pdb=" O ALA C1152 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU C1183 " --> pdb=" O THR C1175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1202 through 1204 Processing sheet with id=AC2, first strand: chain 'B' and resid 33 through 35 removed outlier: 5.742A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N HIS B 91 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 68 through 75 removed outlier: 4.262A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.972A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.076A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 110 through 111 Processing sheet with id=AC7, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.679A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AC9, first strand: chain 'B' and resid 187 through 189 Processing sheet with id=AD1, first strand: chain 'B' and resid 689 through 690 removed outlier: 4.450A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 372 through 376 removed outlier: 4.005A pdb=" N GLY B 372 " --> pdb=" O CYS B 603 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 400 through 404 removed outlier: 3.627A pdb=" N LYS B 400 " --> pdb=" O TYR B 445 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 442 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AD5, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.799A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS B 502 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 724 removed outlier: 7.958A pdb=" N SER B 761 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU B 722 " --> pdb=" O SER B 761 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 768 through 769 removed outlier: 5.490A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1121 through 1129 removed outlier: 5.755A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL B1150 " --> pdb=" O LYS B1174 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1121 through 1129 removed outlier: 5.755A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B1124 " --> pdb=" O VAL B1139 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N HIS B1146 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLU B1148 " --> pdb=" O SER B 781 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N SER B 781 " --> pdb=" O GLU B1148 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL B1150 " --> pdb=" O LYS B 779 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N LYS B 779 " --> pdb=" O VAL B1150 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AE2, first strand: chain 'B' and resid 1202 through 1204 Processing sheet with id=AE3, first strand: chain 'C' and resid 33 through 35 removed outlier: 5.491A pdb=" N ASP C 34 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR C 96 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N HIS C 91 " --> pdb=" O GLN C 98 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.286A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 83 through 85 removed outlier: 5.930A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.256A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'C' and resid 110 through 111 Processing sheet with id=AE8, first strand: chain 'C' and resid 127 through 129 Processing sheet with id=AE9, first strand: chain 'C' and resid 153 through 154 removed outlier: 3.624A pdb=" N ARG C 163 " --> pdb=" O GLY C 154 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 186 through 189 Processing sheet with id=AF2, first strand: chain 'C' and resid 689 through 690 removed outlier: 4.537A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.887A pdb=" N ILE C 442 " --> pdb=" O THR C 574 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 512 through 515 removed outlier: 6.919A pdb=" N THR C 512 " --> pdb=" O LEU C 507 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 502 " --> pdb=" O SER C 557 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TRP C 553 " --> pdb=" O LEU C 506 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C 558 " --> pdb=" O ASP C 539 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 724 removed outlier: 7.885A pdb=" N SER C 761 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU C 722 " --> pdb=" O SER C 761 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AF7, first strand: chain 'C' and resid 1202 through 1204 Processing sheet with id=AF8, first strand: chain 'F' and resid 5 through 6 removed outlier: 3.679A pdb=" N VAL F 5 " --> pdb=" O LYS F 23 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.210A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.742A pdb=" N LEU F 148 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU F 148 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER F 187 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS F 150 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU F 185 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR F 152 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR F 183 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU F 145 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.742A pdb=" N LEU F 148 " --> pdb=" O PHE F 129 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LEU F 148 " --> pdb=" O SER F 187 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER F 187 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LYS F 150 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU F 185 " --> pdb=" O LYS F 150 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR F 152 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR F 183 " --> pdb=" O TYR F 152 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N SER F 184 " --> pdb=" O ALA F 175 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA F 175 " --> pdb=" O SER F 184 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER F 186 " --> pdb=" O PHE F 173 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 157 through 160 Processing sheet with id=AG4, first strand: chain 'F' and resid 201 through 202 Processing sheet with id=AG5, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AG6, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AG7, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.734A pdb=" N SER G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N TYR G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 115 through 119 removed outlier: 3.814A pdb=" N VAL G 134 " --> pdb=" O PHE G 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER G 163 " --> pdb=" O SER G 177 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 154 through 155 removed outlier: 3.518A pdb=" N LYS G 146 " --> pdb=" O THR G 198 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AH2, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.112A pdb=" N GLU H 10 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 127 through 129 removed outlier: 3.539A pdb=" N LEU H 148 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 127 through 129 removed outlier: 3.539A pdb=" N LEU H 148 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N LEU H 148 " --> pdb=" O SER H 187 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER H 187 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS H 150 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LEU H 185 " --> pdb=" O LYS H 150 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N SER H 184 " --> pdb=" O ALA H 175 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA H 175 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER H 186 " --> pdb=" O PHE H 173 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 158 through 160 removed outlier: 4.207A pdb=" N ASN H 204 " --> pdb=" O VAL H 214 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL H 214 " --> pdb=" O ASN H 204 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN H 206 " --> pdb=" O THR H 212 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR H 212 " --> pdb=" O ASN H 206 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.659A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER K 54 " --> pdb=" O TYR K 50 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AH8, first strand: chain 'K' and resid 115 through 119 removed outlier: 4.085A pdb=" N ASN K 139 " --> pdb=" O TYR K 174 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TYR K 174 " --> pdb=" O ASN K 139 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER K 163 " --> pdb=" O SER K 177 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 154 through 155 1246 hydrogen bonds defined for protein. 3373 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.05 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 13754 1.41 - 1.61: 19228 1.61 - 1.82: 216 1.82 - 2.02: 1 2.02 - 2.23: 1 Bond restraints: 33200 Sorted by residual: bond pdb=" CD GLN A 377 " pdb=" OE1 GLN A 377 " ideal model delta sigma weight residual 1.231 1.894 -0.663 1.90e-02 2.77e+03 1.22e+03 bond pdb=" CG GLN A 377 " pdb=" CD GLN A 377 " ideal model delta sigma weight residual 1.516 2.228 -0.712 2.50e-02 1.60e+03 8.11e+02 bond pdb=" CD GLN A 377 " pdb=" NE2 GLN A 377 " ideal model delta sigma weight residual 1.328 1.727 -0.399 2.10e-02 2.27e+03 3.62e+02 bond pdb=" C SER F 160 " pdb=" O SER F 160 " ideal model delta sigma weight residual 1.235 1.367 -0.132 1.14e-02 7.69e+03 1.33e+02 bond pdb=" C SER H 160 " pdb=" O SER H 160 " ideal model delta sigma weight residual 1.236 1.368 -0.132 1.19e-02 7.06e+03 1.23e+02 ... (remaining 33195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 22.33: 45176 22.33 - 44.66: 0 44.66 - 66.98: 0 66.98 - 89.31: 0 89.31 - 111.64: 3 Bond angle restraints: 45179 Sorted by residual: angle pdb=" OE1 GLN A 377 " pdb=" CD GLN A 377 " pdb=" NE2 GLN A 377 " ideal model delta sigma weight residual 122.60 10.96 111.64 1.00e+00 1.00e+00 1.25e+04 angle pdb=" CG GLN A 377 " pdb=" CD GLN A 377 " pdb=" NE2 GLN A 377 " ideal model delta sigma weight residual 116.40 10.05 106.35 1.50e+00 4.44e-01 5.03e+03 angle pdb=" CG GLN A 377 " pdb=" CD GLN A 377 " pdb=" OE1 GLN A 377 " ideal model delta sigma weight residual 120.80 20.68 100.12 2.00e+00 2.50e-01 2.51e+03 angle pdb=" O SER F 186 " pdb=" C SER F 186 " pdb=" CA ASER F 186 " ideal model delta sigma weight residual 120.36 132.31 -11.95 1.08e+00 8.57e-01 1.22e+02 angle pdb=" O SER F 186 " pdb=" C SER F 186 " pdb=" CA BSER F 186 " ideal model delta sigma weight residual 120.36 132.27 -11.91 1.08e+00 8.57e-01 1.22e+02 ... (remaining 45174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.68: 18189 18.68 - 37.36: 1286 37.36 - 56.04: 323 56.04 - 74.72: 57 74.72 - 93.40: 10 Dihedral angle restraints: 19865 sinusoidal: 7579 harmonic: 12286 Sorted by residual: dihedral pdb=" CA LEU A 588 " pdb=" C LEU A 588 " pdb=" N GLU A 589 " pdb=" CA GLU A 589 " ideal model delta harmonic sigma weight residual -180.00 -86.60 -93.40 0 5.00e+00 4.00e-02 3.49e+02 dihedral pdb=" C GLN A 377 " pdb=" N GLN A 377 " pdb=" CA GLN A 377 " pdb=" CB GLN A 377 " ideal model delta harmonic sigma weight residual -122.60 -159.32 36.72 0 2.50e+00 1.60e-01 2.16e+02 dihedral pdb=" N GLN A 377 " pdb=" C GLN A 377 " pdb=" CA GLN A 377 " pdb=" CB GLN A 377 " ideal model delta harmonic sigma weight residual 122.80 158.36 -35.56 0 2.50e+00 1.60e-01 2.02e+02 ... (remaining 19862 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.298: 5045 0.298 - 0.595: 24 0.595 - 0.893: 0 0.893 - 1.190: 1 1.190 - 1.488: 1 Chirality restraints: 5071 Sorted by residual: chirality pdb=" CA GLN A 377 " pdb=" N GLN A 377 " pdb=" C GLN A 377 " pdb=" CB GLN A 377 " both_signs ideal model delta sigma weight residual False 2.51 1.02 1.49 2.00e-01 2.50e+01 5.53e+01 chirality pdb=" CA ASN A 582 " pdb=" N ASN A 582 " pdb=" C ASN A 582 " pdb=" CB ASN A 582 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.30e+01 chirality pdb=" CA ASER H 186 " pdb=" N SER H 186 " pdb=" C SER H 186 " pdb=" CB ASER H 186 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 5068 not shown) Planarity restraints: 5872 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 374 " -0.017 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C VAL A 374 " 0.057 2.00e-02 2.50e+03 pdb=" O VAL A 374 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 375 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 59 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.50e+00 pdb=" C PRO B 59 " -0.044 2.00e-02 2.50e+03 pdb=" O PRO B 59 " 0.017 2.00e-02 2.50e+03 pdb=" N GLN B 60 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 678 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ALA C 678 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA C 678 " -0.016 2.00e-02 2.50e+03 pdb=" N CYS C 679 " -0.015 2.00e-02 2.50e+03 ... (remaining 5869 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.89: 6 1.89 - 2.64: 235 2.64 - 3.39: 41369 3.39 - 4.15: 82364 4.15 - 4.90: 139994 Nonbonded interactions: 263968 Sorted by model distance: nonbonded pdb=" OD2 ASP A 49 " pdb=" NZ LYS A 52 " model vdw 1.135 3.120 nonbonded pdb=" O GLY A 154 " pdb=" CB ARG A 163 " model vdw 1.222 3.440 nonbonded pdb=" CG ASP A 49 " pdb=" NZ LYS A 52 " model vdw 1.237 3.350 nonbonded pdb=" CB ASP A 49 " pdb=" NZ LYS A 52 " model vdw 1.489 3.520 nonbonded pdb=" O GLY A 154 " pdb=" CG ARG A 163 " model vdw 1.806 3.440 ... (remaining 263963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'F' and (resid 1 through 159 or resid 161 through 185 or resid 187 throug \ h 221)) selection = (chain 'H' and (resid 1 through 24 or resid 32 through 159 or resid 161 through \ 185 or resid 187 through 221)) } ncs_group { reference = chain 'G' selection = chain 'K' } 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=0.40 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 32.440 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 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 : 0.014 0.712 33252 Z= 1.042 Angle : 1.755 111.639 45283 Z= 1.350 Chirality : 0.111 1.488 5071 Planarity : 0.004 0.033 5872 Dihedral : 13.582 93.401 11869 Min Nonbonded Distance : 1.135 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.67 % Favored : 96.74 % Rotamer: Outliers : 8.77 % Allowed : 9.49 % Favored : 81.74 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.84 (0.13), residues: 4204 helix: 4.28 (0.18), residues: 744 sheet: 1.71 (0.16), residues: 1043 loop : 0.02 (0.12), residues: 2417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 758 TYR 0.024 0.002 TYR B 635 PHE 0.012 0.002 PHE A 850 TRP 0.013 0.002 TRP H 110 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.01427 (33200) covalent geometry : angle 1.75513 (45179) SS BOND : bond 0.00634 ( 52) SS BOND : angle 1.47043 ( 104) hydrogen bonds : bond 0.20530 ( 1214) hydrogen bonds : angle 7.80212 ( 3373) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 906 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 312 poor density : 594 time to evaluate : 1.221 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: A 91 HIS cc_start: 0.5603 (m170) cc_final: 0.5258 (m170) REVERT: A 164 PHE cc_start: 0.7780 (m-80) cc_final: 0.7214 (m-80) REVERT: A 172 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8328 (pp) REVERT: A 189 PRO cc_start: 0.7837 (Cg_endo) cc_final: 0.7419 (Cg_exo) REVERT: A 234 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7014 (mm) REVERT: A 587 LYS cc_start: 0.1126 (OUTLIER) cc_final: 0.0599 (mmtt) REVERT: A 609 TYR cc_start: 0.4175 (OUTLIER) cc_final: 0.3751 (m-10) REVERT: A 871 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8282 (pp) REVERT: A 960 TRP cc_start: 0.5711 (OUTLIER) cc_final: 0.5081 (p-90) REVERT: B 91 HIS cc_start: 0.5924 (m90) cc_final: 0.5399 (m170) REVERT: B 110 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7634 (mtpt) REVERT: B 172 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8304 (pp) REVERT: B 189 PRO cc_start: 0.7548 (Cg_endo) cc_final: 0.7157 (Cg_exo) REVERT: B 234 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.6987 (mm) REVERT: B 960 TRP cc_start: 0.6401 (OUTLIER) cc_final: 0.5489 (m-90) REVERT: C 815 GLN cc_start: 0.7347 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: C 871 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8111 (pp) REVERT: C 960 TRP cc_start: 0.6254 (OUTLIER) cc_final: 0.5515 (m-90) outliers start: 312 outliers final: 54 residues processed: 846 average time/residue: 0.5898 time to fit residues: 603.6595 Evaluate side-chains 385 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 318 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 828 CYS Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1090 GLU Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 650 CYS Chi-restraints excluded: chain B residue 679 CYS Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 711 VAL Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 960 TRP Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 815 GLN Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 960 TRP Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 6 GLN Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 164 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.0170 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 401 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN A 98 GLN A 167 HIS A 261 GLN A 377 GLN A 618 GLN A 647 ASN A 812 ASN A 988 GLN A1009 GLN A1056 GLN A1145 ASN A1177 ASN A1208 GLN B 98 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 167 HIS B 244 ASN B 277 ASN B 298 HIS B 618 GLN B 637 ASN B 994 GLN B1020 GLN B1056 GLN B1145 ASN B1160 ASN B1177 ASN C 37 GLN C 72 GLN C 167 HIS C 516 GLN C 592 ASN C 618 GLN C 812 ASN C 815 GLN C 819 GLN C 993 ASN C1020 GLN C1132 ASN C1145 ASN C1160 ASN C1177 ASN C1212 GLN F 178 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 148 GLN H 178 GLN K 148 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.127890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.092192 restraints weight = 111215.310| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 3.61 r_work: 0.3303 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33252 Z= 0.155 Angle : 0.654 11.829 45283 Z= 0.353 Chirality : 0.046 0.235 5071 Planarity : 0.004 0.039 5872 Dihedral : 6.833 86.006 4703 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.36 % Favored : 97.43 % Rotamer: Outliers : 5.36 % Allowed : 16.93 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.99 (0.13), residues: 4204 helix: 2.87 (0.18), residues: 767 sheet: 1.03 (0.15), residues: 1142 loop : -0.31 (0.12), residues: 2295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 629 TYR 0.030 0.001 TYR C 445 PHE 0.049 0.002 PHE C 418 TRP 0.033 0.002 TRP F 47 HIS 0.014 0.001 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00334 (33200) covalent geometry : angle 0.65265 (45179) SS BOND : bond 0.00305 ( 52) SS BOND : angle 1.19196 ( 104) hydrogen bonds : bond 0.06301 ( 1214) hydrogen bonds : angle 5.88254 ( 3373) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 327 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 172 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8315 (pp) REVERT: A 251 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8690 (tp) REVERT: A 587 LYS cc_start: 0.0229 (OUTLIER) cc_final: -0.0063 (mmtt) REVERT: A 1175 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7319 (p) REVERT: B 164 PHE cc_start: 0.7476 (m-10) cc_final: 0.7257 (m-80) REVERT: B 172 LEU cc_start: 0.8665 (pp) cc_final: 0.8412 (pp) REVERT: B 545 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8074 (mp) REVERT: B 686 MET cc_start: 0.8984 (tpt) cc_final: 0.8422 (mmp) REVERT: C 110 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7567 (mtpt) REVERT: C 569 MET cc_start: 0.7671 (mpp) cc_final: 0.6745 (mmp) REVERT: C 628 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6416 (mt0) REVERT: C 808 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8472 (tp40) REVERT: C 1180 ILE cc_start: 0.4478 (OUTLIER) cc_final: 0.4079 (pp) REVERT: F 131 LEU cc_start: -0.5576 (OUTLIER) cc_final: -0.5782 (mp) REVERT: H 29 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.5770 (t80) REVERT: H 81 MET cc_start: 0.8189 (ttt) cc_final: 0.7970 (ttm) REVERT: K 40 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8362 (mmm-85) REVERT: K 168 ASP cc_start: 0.8061 (t0) cc_final: 0.7824 (t0) outliers start: 189 outliers final: 84 residues processed: 493 average time/residue: 0.5821 time to fit residues: 349.2594 Evaluate side-chains 348 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 253 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ASP Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 208 HIS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1041 SER Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1180 ILE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 111 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 137 optimal weight: 0.9990 chunk 268 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 221 optimal weight: 0.3980 chunk 162 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 315 optimal weight: 1.9990 chunk 312 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN A 280 GLN A 994 GLN A1110 GLN B 98 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 280 GLN C 91 HIS C 471 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 178 GLN H 199 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.124444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.087019 restraints weight = 120068.258| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.85 r_work: 0.3192 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33252 Z= 0.149 Angle : 0.616 10.265 45283 Z= 0.326 Chirality : 0.045 0.371 5071 Planarity : 0.004 0.045 5872 Dihedral : 6.164 87.937 4661 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.74 % Favored : 96.95 % Rotamer: Outliers : 5.30 % Allowed : 17.60 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.62 (0.12), residues: 4204 helix: 2.42 (0.19), residues: 770 sheet: 0.81 (0.15), residues: 1122 loop : -0.48 (0.12), residues: 2312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1057 TYR 0.024 0.001 TYR C 445 PHE 0.020 0.002 PHE C 418 TRP 0.040 0.001 TRP F 47 HIS 0.007 0.001 HIS C 208 Details of bonding type rmsd covalent geometry : bond 0.00330 (33200) covalent geometry : angle 0.61459 (45179) SS BOND : bond 0.00574 ( 52) SS BOND : angle 1.11914 ( 104) hydrogen bonds : bond 0.05316 ( 1214) hydrogen bonds : angle 5.28363 ( 3373) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 279 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.6671 (OUTLIER) cc_final: 0.5216 (m-80) REVERT: A 235 ARG cc_start: 0.7443 (mmt-90) cc_final: 0.6934 (mmt-90) REVERT: A 251 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8852 (tp) REVERT: A 587 LYS cc_start: -0.0082 (OUTLIER) cc_final: -0.0337 (mmtm) REVERT: A 872 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8920 (p) REVERT: A 1175 THR cc_start: 0.7748 (OUTLIER) cc_final: 0.7520 (p) REVERT: B 67 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8656 (pp) REVERT: B 110 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7712 (mtpt) REVERT: B 172 LEU cc_start: 0.8705 (pp) cc_final: 0.8491 (pp) REVERT: B 184 TYR cc_start: 0.6389 (OUTLIER) cc_final: 0.5541 (m-80) REVERT: B 235 ARG cc_start: 0.7309 (mmp80) cc_final: 0.6727 (mmp80) REVERT: B 545 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8208 (mp) REVERT: B 686 MET cc_start: 0.9152 (tpt) cc_final: 0.8604 (mmp) REVERT: B 698 LYS cc_start: 0.8454 (mmmm) cc_final: 0.8164 (tppt) REVERT: C 110 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7664 (mtpt) REVERT: C 148 MET cc_start: 0.8970 (ttm) cc_final: 0.8674 (ttm) REVERT: C 408 ASN cc_start: 0.8247 (m-40) cc_final: 0.7760 (t0) REVERT: C 569 MET cc_start: 0.7554 (mpp) cc_final: 0.6656 (mmp) REVERT: C 628 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6409 (mt0) REVERT: C 808 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8423 (tp40) REVERT: F 48 MET cc_start: 0.8374 (mmm) cc_final: 0.7999 (mpt) REVERT: H 29 PHE cc_start: 0.6671 (OUTLIER) cc_final: 0.6003 (t80) REVERT: H 99 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6595 (pp20) REVERT: K 27 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.8120 (tm-30) REVERT: K 40 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8424 (mmm-85) REVERT: K 64 SER cc_start: 0.7600 (OUTLIER) cc_final: 0.7385 (p) REVERT: K 76 ILE cc_start: 0.6178 (mp) cc_final: 0.5792 (mt) REVERT: K 101 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7056 (mt0) outliers start: 187 outliers final: 86 residues processed: 441 average time/residue: 0.5341 time to fit residues: 291.2019 Evaluate side-chains 340 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 237 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1038 SER Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 820 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain K residue 164 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 173 optimal weight: 4.9990 chunk 416 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 155 optimal weight: 0.4980 chunk 328 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 272 optimal weight: 20.0000 chunk 108 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 582 ASN A 993 ASN A1110 GLN A1132 ASN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 HIS B 637 ASN B1056 GLN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 647 ASN C1029 ASN C1132 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** H 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.118613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081299 restraints weight = 114994.890| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.78 r_work: 0.3061 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 33252 Z= 0.294 Angle : 0.702 9.797 45283 Z= 0.374 Chirality : 0.050 0.483 5071 Planarity : 0.005 0.056 5872 Dihedral : 6.255 87.800 4641 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.48 % Favored : 96.26 % Rotamer: Outliers : 5.52 % Allowed : 17.65 % Favored : 76.82 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: 0.10 (0.12), residues: 4204 helix: 1.87 (0.19), residues: 746 sheet: 0.44 (0.15), residues: 1180 loop : -0.75 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1113 TYR 0.023 0.002 TYR B 469 PHE 0.020 0.002 PHE B 865 TRP 0.034 0.002 TRP F 47 HIS 0.011 0.002 HIS B1138 Details of bonding type rmsd covalent geometry : bond 0.00703 (33200) covalent geometry : angle 0.69774 (45179) SS BOND : bond 0.00391 ( 52) SS BOND : angle 1.69374 ( 104) hydrogen bonds : bond 0.06603 ( 1214) hydrogen bonds : angle 5.58126 ( 3373) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 260 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.6729 (OUTLIER) cc_final: 0.4993 (m-80) REVERT: A 225 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8528 (tp) REVERT: A 587 LYS cc_start: -0.0529 (OUTLIER) cc_final: -0.0826 (mmtt) REVERT: A 609 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.6567 (t80) REVERT: A 872 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8878 (p) REVERT: A 907 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7359 (pp30) REVERT: A 1175 THR cc_start: 0.7865 (OUTLIER) cc_final: 0.7646 (t) REVERT: B 110 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7643 (mtpt) REVERT: B 184 TYR cc_start: 0.6468 (OUTLIER) cc_final: 0.5481 (m-80) REVERT: B 219 TYR cc_start: 0.8268 (m-80) cc_final: 0.7910 (m-80) REVERT: B 545 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8203 (mp) REVERT: B 623 VAL cc_start: 0.8961 (OUTLIER) cc_final: 0.8623 (m) REVERT: B 698 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8422 (tppt) REVERT: B 1008 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7226 (tpt) REVERT: B 1105 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8476 (tt0) REVERT: C 110 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7781 (mtpt) REVERT: C 184 TYR cc_start: 0.5922 (OUTLIER) cc_final: 0.4972 (m-80) REVERT: C 569 MET cc_start: 0.7551 (mpp) cc_final: 0.6818 (mmp) REVERT: C 628 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.6666 (mt0) REVERT: C 808 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8386 (tp40) REVERT: C 815 GLN cc_start: 0.8524 (mt0) cc_final: 0.8313 (mp10) REVERT: F 118 VAL cc_start: 0.0378 (OUTLIER) cc_final: 0.0140 (t) REVERT: H 29 PHE cc_start: 0.6996 (OUTLIER) cc_final: 0.6441 (t80) REVERT: H 99 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6841 (pp20) REVERT: H 162 ASN cc_start: 0.5743 (m-40) cc_final: 0.5524 (m-40) REVERT: K 64 SER cc_start: 0.7606 (OUTLIER) cc_final: 0.7369 (p) REVERT: K 68 SER cc_start: 0.6257 (p) cc_final: 0.5918 (t) REVERT: K 88 TYR cc_start: 0.8592 (m-80) cc_final: 0.8147 (m-80) REVERT: K 101 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7081 (mt0) REVERT: K 109 ARG cc_start: 0.7069 (pmt170) cc_final: 0.6791 (pmt170) outliers start: 195 outliers final: 99 residues processed: 427 average time/residue: 0.5631 time to fit residues: 295.1049 Evaluate side-chains 346 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 225 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 679 CYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 872 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1008 MET Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 131 ILE Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 682 ILE Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 1015 THR Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 99 GLU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 64 SER Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 101 GLN Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 401 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 402 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 391 optimal weight: 3.9990 chunk 367 optimal weight: 8.9990 chunk 245 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 344 optimal weight: 20.0000 chunk 219 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B 576 GLN B 993 ASN B1217 ASN C 408 ASN C 519 ASN C1029 ASN C1132 ASN F 62 GLN ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.116973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.079812 restraints weight = 98993.805| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 3.41 r_work: 0.3049 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3040 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3040 r_free = 0.3040 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3040 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 33252 Z= 0.281 Angle : 0.690 11.573 45283 Z= 0.366 Chirality : 0.050 0.546 5071 Planarity : 0.005 0.059 5872 Dihedral : 6.231 89.789 4637 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.79 % Favored : 95.93 % Rotamer: Outliers : 5.66 % Allowed : 17.96 % Favored : 76.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: -0.22 (0.12), residues: 4204 helix: 1.61 (0.19), residues: 742 sheet: 0.17 (0.15), residues: 1179 loop : -0.92 (0.12), residues: 2283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1057 TYR 0.023 0.002 TYR C 497 PHE 0.018 0.002 PHE B 850 TRP 0.044 0.002 TRP F 47 HIS 0.008 0.002 HIS C1138 Details of bonding type rmsd covalent geometry : bond 0.00671 (33200) covalent geometry : angle 0.68619 (45179) SS BOND : bond 0.00679 ( 52) SS BOND : angle 1.66900 ( 104) hydrogen bonds : bond 0.06447 ( 1214) hydrogen bonds : angle 5.60691 ( 3373) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 240 time to evaluate : 1.169 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: A 184 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.5064 (m-80) REVERT: A 225 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8542 (tp) REVERT: A 235 ARG cc_start: 0.7408 (mmt-90) cc_final: 0.6954 (mmt-90) REVERT: A 609 TYR cc_start: 0.7772 (OUTLIER) cc_final: 0.7438 (t80) REVERT: A 635 TYR cc_start: 0.8517 (m-80) cc_final: 0.8141 (m-80) REVERT: A 700 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7002 (pmt-80) REVERT: A 728 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.8881 (mmmt) REVERT: A 907 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7432 (pp30) REVERT: A 988 GLN cc_start: 0.8755 (tt0) cc_final: 0.8510 (tp40) REVERT: B 110 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7690 (mtpt) REVERT: B 174 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6855 (m-30) REVERT: B 184 TYR cc_start: 0.6727 (OUTLIER) cc_final: 0.5500 (m-80) REVERT: B 291 LYS cc_start: 0.8773 (mtmp) cc_final: 0.8401 (mtmm) REVERT: B 545 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8163 (mp) REVERT: B 623 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8608 (m) REVERT: B 698 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8531 (tppt) REVERT: B 1105 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: C 110 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7854 (mtpt) REVERT: C 184 TYR cc_start: 0.5944 (OUTLIER) cc_final: 0.4953 (m-80) REVERT: C 569 MET cc_start: 0.7544 (mpp) cc_final: 0.6667 (mmp) REVERT: C 628 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.6706 (mt0) REVERT: C 808 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8368 (tp40) REVERT: C 815 GLN cc_start: 0.8493 (mt0) cc_final: 0.8267 (mp10) REVERT: F 48 MET cc_start: 0.7859 (mpp) cc_final: 0.7338 (mpt) REVERT: F 118 VAL cc_start: 0.0391 (OUTLIER) cc_final: 0.0104 (t) REVERT: H 29 PHE cc_start: 0.7410 (OUTLIER) cc_final: 0.6935 (t80) REVERT: H 162 ASN cc_start: 0.6355 (m-40) cc_final: 0.6000 (m-40) REVERT: K 27 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: K 55 ARG cc_start: 0.7465 (mpt-90) cc_final: 0.7073 (mmt90) REVERT: K 68 SER cc_start: 0.5877 (p) cc_final: 0.5576 (t) REVERT: K 76 ILE cc_start: 0.6134 (OUTLIER) cc_final: 0.5719 (mt) REVERT: K 88 TYR cc_start: 0.8604 (m-80) cc_final: 0.8188 (m-80) outliers start: 200 outliers final: 107 residues processed: 413 average time/residue: 0.6010 time to fit residues: 301.0026 Evaluate side-chains 335 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 208 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 612 SER Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 877 VAL Chi-restraints excluded: chain A residue 907 GLN Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1175 THR Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 334 ARG Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 495 LEU Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 893 LEU Chi-restraints excluded: chain B residue 929 VAL Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 983 VAL Chi-restraints excluded: chain B residue 1015 THR Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1055 ILE Chi-restraints excluded: chain B residue 1105 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 495 LEU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 621 THR Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 829 SER Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 1054 ILE Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 61 ASP Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 83 ASP Chi-restraints excluded: chain K residue 98 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 147 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 213 optimal weight: 0.0570 chunk 199 optimal weight: 4.9990 chunk 292 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 409 optimal weight: 0.9990 chunk 392 optimal weight: 0.2980 chunk 233 optimal weight: 20.0000 chunk 284 optimal weight: 2.9990 chunk 316 optimal weight: 0.5980 chunk 343 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 708 GLN A1110 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 GLN B1056 GLN B1072 ASN B1110 GLN B1217 ASN C 107 GLN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.120062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.083620 restraints weight = 107635.984| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.69 r_work: 0.3114 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 33252 Z= 0.126 Angle : 0.613 13.117 45283 Z= 0.319 Chirality : 0.045 0.581 5071 Planarity : 0.004 0.057 5872 Dihedral : 5.609 89.929 4630 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.57 % Favored : 96.19 % Rotamer: Outliers : 3.94 % Allowed : 20.07 % Favored : 75.99 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.13), residues: 4204 helix: 1.93 (0.19), residues: 757 sheet: 0.26 (0.15), residues: 1155 loop : -0.77 (0.12), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1057 TYR 0.023 0.001 TYR C 445 PHE 0.016 0.001 PHE A 977 TRP 0.042 0.001 TRP F 47 HIS 0.007 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00279 (33200) covalent geometry : angle 0.60773 (45179) SS BOND : bond 0.00949 ( 52) SS BOND : angle 1.83039 ( 104) hydrogen bonds : bond 0.04741 ( 1214) hydrogen bonds : angle 5.13615 ( 3373) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 232 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.4933 (m-80) REVERT: A 609 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.7010 (t80) REVERT: A 988 GLN cc_start: 0.8685 (tt0) cc_final: 0.8418 (tp40) REVERT: B 110 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7516 (mtpt) REVERT: B 184 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.5493 (m-80) REVERT: B 545 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8208 (mp) REVERT: B 623 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8602 (m) REVERT: B 698 LYS cc_start: 0.8665 (mmmm) cc_final: 0.8397 (tppt) REVERT: B 1090 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8067 (mp0) REVERT: C 110 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7758 (mtpt) REVERT: C 184 TYR cc_start: 0.5981 (OUTLIER) cc_final: 0.5058 (m-80) REVERT: C 569 MET cc_start: 0.7554 (mpp) cc_final: 0.6825 (mmp) REVERT: C 628 GLN cc_start: 0.7604 (OUTLIER) cc_final: 0.6490 (mm-40) REVERT: C 808 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8294 (tp40) REVERT: C 815 GLN cc_start: 0.8424 (mt0) cc_final: 0.8201 (mp10) REVERT: F 47 TRP cc_start: 0.8341 (t60) cc_final: 0.8074 (t60) REVERT: F 48 MET cc_start: 0.7849 (mpp) cc_final: 0.7333 (mpt) REVERT: F 118 VAL cc_start: 0.0357 (OUTLIER) cc_final: 0.0072 (t) REVERT: H 29 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6679 (t80) REVERT: K 11 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8026 (pt) REVERT: K 68 SER cc_start: 0.6031 (p) cc_final: 0.5770 (t) REVERT: K 88 TYR cc_start: 0.8416 (m-80) cc_final: 0.7942 (m-80) outliers start: 138 outliers final: 64 residues processed: 350 average time/residue: 0.5825 time to fit residues: 247.8725 Evaluate side-chains 286 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 208 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 688 GLN Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 844 ASP Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 877 VAL Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 194 optimal weight: 0.0270 chunk 327 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 351 optimal weight: 20.0000 chunk 409 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 210 optimal weight: 4.9990 chunk 235 optimal weight: 2.9990 chunk 406 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 295 optimal weight: 3.9990 overall best weight: 0.9244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 708 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1110 GLN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.119593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.080677 restraints weight = 120098.969| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.82 r_work: 0.3098 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3073 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 33252 Z= 0.138 Angle : 0.608 12.530 45283 Z= 0.315 Chirality : 0.044 0.558 5071 Planarity : 0.004 0.054 5872 Dihedral : 5.473 88.118 4626 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.81 % Favored : 95.95 % Rotamer: Outliers : 4.00 % Allowed : 20.15 % Favored : 75.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.03 (0.13), residues: 4204 helix: 2.03 (0.19), residues: 753 sheet: 0.19 (0.14), residues: 1179 loop : -0.76 (0.12), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 24 TYR 0.020 0.001 TYR C 445 PHE 0.016 0.001 PHE B 232 TRP 0.035 0.001 TRP F 47 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00320 (33200) covalent geometry : angle 0.60317 (45179) SS BOND : bond 0.00508 ( 52) SS BOND : angle 1.67981 ( 104) hydrogen bonds : bond 0.04867 ( 1214) hydrogen bonds : angle 5.08217 ( 3373) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 222 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 TYR cc_start: 0.6549 (OUTLIER) cc_final: 0.4993 (m-80) REVERT: A 609 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.7177 (t80) REVERT: A 700 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6828 (pmt-80) REVERT: A 988 GLN cc_start: 0.8702 (tt0) cc_final: 0.8450 (tp40) REVERT: B 110 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7611 (mtpt) REVERT: B 184 TYR cc_start: 0.6565 (OUTLIER) cc_final: 0.5603 (m-80) REVERT: B 235 ARG cc_start: 0.7422 (mmp80) cc_final: 0.7024 (mmp80) REVERT: B 291 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8477 (mtmm) REVERT: B 545 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8204 (mp) REVERT: B 623 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8627 (m) REVERT: B 698 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8489 (tppt) REVERT: B 891 GLU cc_start: 0.8684 (tt0) cc_final: 0.8447 (tt0) REVERT: B 1090 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8186 (mp0) REVERT: C 110 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7844 (mtpt) REVERT: C 184 TYR cc_start: 0.6021 (OUTLIER) cc_final: 0.5037 (m-80) REVERT: C 569 MET cc_start: 0.7657 (mpp) cc_final: 0.6909 (mmp) REVERT: C 628 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6344 (mm-40) REVERT: C 808 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8309 (tp40) REVERT: C 815 GLN cc_start: 0.8474 (mt0) cc_final: 0.8268 (mp10) REVERT: F 48 MET cc_start: 0.7861 (mpp) cc_final: 0.7410 (mpt) REVERT: F 118 VAL cc_start: 0.0241 (OUTLIER) cc_final: -0.0029 (t) REVERT: G 101 GLN cc_start: 0.5753 (mp10) cc_final: 0.5276 (pp30) REVERT: H 29 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6603 (t80) REVERT: H 70 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8553 (mt) REVERT: K 11 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7959 (pt) REVERT: K 27 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: K 68 SER cc_start: 0.6219 (p) cc_final: 0.5943 (t) outliers start: 140 outliers final: 80 residues processed: 347 average time/residue: 0.5722 time to fit residues: 242.3930 Evaluate side-chains 309 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 211 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 366 optimal weight: 6.9990 chunk 232 optimal weight: 7.9990 chunk 254 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 264 optimal weight: 20.0000 chunk 116 optimal weight: 0.9990 chunk 296 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 384 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 258 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 812 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 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 = 0.4016 r_free = 0.4016 target = 0.119149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.082262 restraints weight = 106957.100| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 3.42 r_work: 0.3082 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 33252 Z= 0.151 Angle : 0.625 14.065 45283 Z= 0.323 Chirality : 0.045 0.565 5071 Planarity : 0.004 0.054 5872 Dihedral : 5.275 50.382 4622 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.90 % Favored : 95.86 % Rotamer: Outliers : 3.86 % Allowed : 20.51 % Favored : 75.63 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.13), residues: 4204 helix: 1.95 (0.19), residues: 754 sheet: 0.15 (0.14), residues: 1180 loop : -0.77 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 700 TYR 0.026 0.001 TYR H 32 PHE 0.018 0.001 PHE B 232 TRP 0.045 0.001 TRP F 47 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00354 (33200) covalent geometry : angle 0.61895 (45179) SS BOND : bond 0.00526 ( 52) SS BOND : angle 1.92746 ( 104) hydrogen bonds : bond 0.04964 ( 1214) hydrogen bonds : angle 5.10071 ( 3373) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 219 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.7794 (mtpt) REVERT: A 184 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.5110 (m-80) REVERT: A 609 TYR cc_start: 0.7710 (OUTLIER) cc_final: 0.7262 (t80) REVERT: A 700 ARG cc_start: 0.7232 (OUTLIER) cc_final: 0.6835 (pmt-80) REVERT: B 110 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7580 (mtpt) REVERT: B 184 TYR cc_start: 0.6398 (OUTLIER) cc_final: 0.5625 (m-80) REVERT: B 545 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8177 (mp) REVERT: B 623 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8643 (m) REVERT: B 698 LYS cc_start: 0.8745 (mmmm) cc_final: 0.8544 (tppt) REVERT: B 1090 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: C 110 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7848 (mtpt) REVERT: C 184 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.5060 (m-80) REVERT: C 497 TYR cc_start: 0.6923 (m-80) cc_final: 0.6531 (m-80) REVERT: C 569 MET cc_start: 0.7520 (mpp) cc_final: 0.6880 (mmp) REVERT: C 628 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.6392 (mm-40) REVERT: C 808 GLN cc_start: 0.9103 (OUTLIER) cc_final: 0.8289 (tp40) REVERT: C 815 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8226 (mp10) REVERT: F 47 TRP cc_start: 0.8335 (t60) cc_final: 0.7967 (t60) REVERT: F 48 MET cc_start: 0.7810 (mpp) cc_final: 0.6940 (mpt) REVERT: F 118 VAL cc_start: 0.0143 (OUTLIER) cc_final: -0.0178 (t) REVERT: G 101 GLN cc_start: 0.5673 (mp10) cc_final: 0.5063 (pp30) REVERT: H 29 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6803 (t80) REVERT: K 27 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7953 (tm-30) REVERT: K 68 SER cc_start: 0.6104 (p) cc_final: 0.5835 (t) REVERT: K 88 TYR cc_start: 0.8584 (m-80) cc_final: 0.8118 (m-80) REVERT: K 168 ASP cc_start: 0.8384 (t0) cc_final: 0.8109 (t0) outliers start: 135 outliers final: 90 residues processed: 342 average time/residue: 0.5994 time to fit residues: 249.2592 Evaluate side-chains 315 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 208 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1054 ILE Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 815 GLN Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 900 ILE Chi-restraints excluded: chain C residue 913 MET Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 193 optimal weight: 0.7980 chunk 376 optimal weight: 1.9990 chunk 360 optimal weight: 30.0000 chunk 271 optimal weight: 20.0000 chunk 214 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 185 optimal weight: 0.1980 chunk 265 optimal weight: 0.0030 chunk 165 optimal weight: 8.9990 chunk 242 optimal weight: 4.9990 chunk 292 optimal weight: 0.6980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 708 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.119873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.082205 restraints weight = 149178.215| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 4.60 r_work: 0.3074 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 33252 Z= 0.131 Angle : 0.626 13.337 45283 Z= 0.322 Chirality : 0.045 0.565 5071 Planarity : 0.004 0.054 5872 Dihedral : 5.203 51.065 4622 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.86 % Favored : 95.98 % Rotamer: Outliers : 3.50 % Allowed : 21.07 % Favored : 75.44 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.01 (0.13), residues: 4204 helix: 1.99 (0.19), residues: 756 sheet: 0.16 (0.14), residues: 1174 loop : -0.76 (0.12), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 542 TYR 0.026 0.001 TYR H 32 PHE 0.019 0.001 PHE B 232 TRP 0.042 0.001 TRP F 47 HIS 0.006 0.001 HIS A 208 Details of bonding type rmsd covalent geometry : bond 0.00306 (33200) covalent geometry : angle 0.61897 (45179) SS BOND : bond 0.00538 ( 52) SS BOND : angle 2.05431 ( 104) hydrogen bonds : bond 0.04633 ( 1214) hydrogen bonds : angle 5.01940 ( 3373) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 220 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.7775 (mtpt) REVERT: A 184 TYR cc_start: 0.6813 (OUTLIER) cc_final: 0.5079 (m-80) REVERT: A 700 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6896 (pmt-80) REVERT: B 110 LYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7574 (mtpt) REVERT: B 184 TYR cc_start: 0.6629 (OUTLIER) cc_final: 0.5663 (m-80) REVERT: B 235 ARG cc_start: 0.7293 (mmp80) cc_final: 0.6933 (mmp80) REVERT: B 291 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8700 (mtmp) REVERT: B 545 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8193 (mp) REVERT: B 623 VAL cc_start: 0.8960 (OUTLIER) cc_final: 0.8651 (m) REVERT: B 698 LYS cc_start: 0.8748 (mmmm) cc_final: 0.8523 (tppt) REVERT: B 1090 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8295 (mp0) REVERT: C 110 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7871 (mtpt) REVERT: C 184 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.5063 (m-80) REVERT: C 497 TYR cc_start: 0.6950 (m-80) cc_final: 0.6552 (m-80) REVERT: C 569 MET cc_start: 0.7483 (mpp) cc_final: 0.6890 (mmp) REVERT: C 628 GLN cc_start: 0.7442 (OUTLIER) cc_final: 0.6359 (mm-40) REVERT: C 808 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8295 (tp40) REVERT: C 815 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: F 48 MET cc_start: 0.7817 (mpp) cc_final: 0.7114 (mpt) REVERT: F 118 VAL cc_start: 0.0116 (OUTLIER) cc_final: -0.0187 (t) REVERT: G 43 GLN cc_start: 0.5243 (OUTLIER) cc_final: 0.5022 (pp30) REVERT: G 101 GLN cc_start: 0.5631 (mp10) cc_final: 0.5029 (pp30) REVERT: H 29 PHE cc_start: 0.7387 (OUTLIER) cc_final: 0.7145 (t80) REVERT: H 70 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8527 (mt) REVERT: K 27 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: K 68 SER cc_start: 0.6316 (p) cc_final: 0.6010 (t) REVERT: K 88 TYR cc_start: 0.8553 (m-80) cc_final: 0.8107 (m-80) REVERT: K 168 ASP cc_start: 0.8395 (t0) cc_final: 0.8101 (t0) outliers start: 122 outliers final: 84 residues processed: 329 average time/residue: 0.6077 time to fit residues: 242.8319 Evaluate side-chains 312 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 209 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 816 LYS Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1090 GLU Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 815 GLN Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 285 optimal weight: 1.9990 chunk 155 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 269 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 347 optimal weight: 10.0000 chunk 164 optimal weight: 6.9990 chunk 300 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 708 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.118621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.081518 restraints weight = 155685.392| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 4.85 r_work: 0.3032 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 33252 Z= 0.172 Angle : 0.646 13.281 45283 Z= 0.334 Chirality : 0.045 0.544 5071 Planarity : 0.004 0.054 5872 Dihedral : 5.231 50.311 4618 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.21 % Favored : 95.62 % Rotamer: Outliers : 3.50 % Allowed : 21.09 % Favored : 75.41 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.06 (0.13), residues: 4204 helix: 1.94 (0.19), residues: 753 sheet: 0.12 (0.14), residues: 1200 loop : -0.81 (0.12), residues: 2251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 921 TYR 0.023 0.001 TYR H 32 PHE 0.020 0.002 PHE B 232 TRP 0.049 0.001 TRP F 47 HIS 0.006 0.001 HIS A1138 Details of bonding type rmsd covalent geometry : bond 0.00409 (33200) covalent geometry : angle 0.64004 (45179) SS BOND : bond 0.00564 ( 52) SS BOND : angle 1.96356 ( 104) hydrogen bonds : bond 0.05203 ( 1214) hydrogen bonds : angle 5.13578 ( 3373) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8408 Ramachandran restraints generated. 4204 Oldfield, 0 Emsley, 4204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 210 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7821 (mtpt) REVERT: A 184 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.5151 (m-80) REVERT: A 700 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7003 (pmt-80) REVERT: B 62 ARG cc_start: 0.6576 (mmm-85) cc_final: 0.6288 (mmm-85) REVERT: B 110 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7606 (mtpt) REVERT: B 184 TYR cc_start: 0.6471 (OUTLIER) cc_final: 0.5516 (m-80) REVERT: B 235 ARG cc_start: 0.7200 (mmp80) cc_final: 0.6788 (mmp80) REVERT: B 291 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8713 (mtmp) REVERT: B 545 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8242 (mp) REVERT: B 623 VAL cc_start: 0.9004 (OUTLIER) cc_final: 0.8689 (m) REVERT: B 698 LYS cc_start: 0.8815 (mmmm) cc_final: 0.8566 (tppt) REVERT: B 1008 MET cc_start: 0.8406 (tmm) cc_final: 0.7916 (ttp) REVERT: C 110 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7928 (mtpt) REVERT: C 184 TYR cc_start: 0.6094 (OUTLIER) cc_final: 0.5084 (m-80) REVERT: C 497 TYR cc_start: 0.6985 (m-80) cc_final: 0.6353 (m-80) REVERT: C 563 MET cc_start: 0.4766 (tpp) cc_final: 0.4286 (tpp) REVERT: C 569 MET cc_start: 0.7617 (mpp) cc_final: 0.6945 (mmp) REVERT: C 628 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.6420 (mm-40) REVERT: C 808 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8330 (tp40) REVERT: C 815 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: F 47 TRP cc_start: 0.8106 (t60) cc_final: 0.7799 (t60) REVERT: F 48 MET cc_start: 0.7819 (mpp) cc_final: 0.7096 (mpt) REVERT: F 118 VAL cc_start: 0.0137 (OUTLIER) cc_final: -0.0161 (t) REVERT: G 43 GLN cc_start: 0.5220 (OUTLIER) cc_final: 0.5005 (pp30) REVERT: G 101 GLN cc_start: 0.5691 (mp10) cc_final: 0.5127 (pp30) REVERT: H 2 VAL cc_start: 0.7533 (OUTLIER) cc_final: 0.7309 (p) REVERT: H 29 PHE cc_start: 0.7530 (OUTLIER) cc_final: 0.7270 (t80) REVERT: H 70 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8557 (mt) REVERT: K 27 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7877 (tm-30) REVERT: K 68 SER cc_start: 0.6312 (p) cc_final: 0.5995 (t) REVERT: K 88 TYR cc_start: 0.8581 (m-80) cc_final: 0.8149 (m-80) REVERT: K 168 ASP cc_start: 0.8486 (t0) cc_final: 0.8194 (t0) outliers start: 122 outliers final: 91 residues processed: 319 average time/residue: 0.6089 time to fit residues: 236.0123 Evaluate side-chains 315 residues out of total 3614 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 205 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LYS Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 110 LYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 TYR Chi-restraints excluded: chain A residue 294 SER Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 609 TYR Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 736 CYS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 771 ASP Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 960 TRP Chi-restraints excluded: chain A residue 983 VAL Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1031 GLN Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 184 TYR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 438 TYR Chi-restraints excluded: chain B residue 502 LYS Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 623 VAL Chi-restraints excluded: chain B residue 662 ILE Chi-restraints excluded: chain B residue 682 ILE Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 734 SER Chi-restraints excluded: chain B residue 779 LYS Chi-restraints excluded: chain B residue 829 SER Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1043 THR Chi-restraints excluded: chain B residue 1180 ILE Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 143 ILE Chi-restraints excluded: chain C residue 156 PHE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 184 TYR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 420 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 496 LYS Chi-restraints excluded: chain C residue 526 CYS Chi-restraints excluded: chain C residue 530 VAL Chi-restraints excluded: chain C residue 623 VAL Chi-restraints excluded: chain C residue 628 GLN Chi-restraints excluded: chain C residue 679 CYS Chi-restraints excluded: chain C residue 696 MET Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 734 SER Chi-restraints excluded: chain C residue 808 GLN Chi-restraints excluded: chain C residue 815 GLN Chi-restraints excluded: chain C residue 871 LEU Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 1005 LEU Chi-restraints excluded: chain C residue 1216 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 70 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 190 HIS Chi-restraints excluded: chain G residue 192 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 59 ILE Chi-restraints excluded: chain K residue 76 ILE Chi-restraints excluded: chain K residue 105 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 132 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 172 SER Chi-restraints excluded: chain K residue 197 VAL Chi-restraints excluded: chain K residue 206 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 422 random chunks: chunk 296 optimal weight: 2.9990 chunk 389 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 409 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 284 optimal weight: 4.9990 chunk 320 optimal weight: 1.9990 chunk 315 optimal weight: 0.0870 chunk 33 optimal weight: 2.9990 chunk 311 optimal weight: 0.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 HIS A 708 GLN ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS C 194 HIS ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.119388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.081283 restraints weight = 137124.142| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.17 r_work: 0.3077 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3068 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 33252 Z= 0.138 Angle : 0.627 13.364 45283 Z= 0.322 Chirality : 0.044 0.512 5071 Planarity : 0.004 0.052 5872 Dihedral : 5.105 50.999 4618 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.05 % Favored : 95.79 % Rotamer: Outliers : 3.41 % Allowed : 21.12 % Favored : 75.46 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.83 % Cis-general : 0.15 % 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: 0.00 (0.13), residues: 4204 helix: 2.02 (0.19), residues: 751 sheet: 0.16 (0.14), residues: 1189 loop : -0.78 (0.12), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 55 TYR 0.027 0.001 TYR C 445 PHE 0.018 0.001 PHE B 590 TRP 0.043 0.001 TRP F 47 HIS 0.006 0.001 HIS B 208 Details of bonding type rmsd covalent geometry : bond 0.00323 (33200) covalent geometry : angle 0.62185 (45179) SS BOND : bond 0.00490 ( 52) SS BOND : angle 1.76313 ( 104) hydrogen bonds : bond 0.04736 ( 1214) hydrogen bonds : angle 5.04279 ( 3373) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17706.24 seconds wall clock time: 300 minutes 31.89 seconds (18031.89 seconds total)