Starting phenix.real_space_refine on Wed Feb 21 01:44:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjy_32552/02_2024/7wjy_32552.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjy_32552/02_2024/7wjy_32552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjy_32552/02_2024/7wjy_32552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjy_32552/02_2024/7wjy_32552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjy_32552/02_2024/7wjy_32552.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wjy_32552/02_2024/7wjy_32552.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 125 5.16 5 C 18774 2.51 5 N 4886 2.21 5 O 5644 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 237": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "B ARG 16": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 72": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 96": "NH1" <-> "NH2" Residue "D ARG 237": "NH1" <-> "NH2" Residue "D ARG 346": "NH1" <-> "NH2" Residue "D ARG 408": "NH1" <-> "NH2" Residue "D ARG 454": "NH1" <-> "NH2" Residue "D ARG 457": "NH1" <-> "NH2" Residue "D ARG 466": "NH1" <-> "NH2" Residue "D PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 988": "OE1" <-> "OE2" Residue "E ARG 16": "NH1" <-> "NH2" Residue "E ARG 19": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "G PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 237": "NH1" <-> "NH2" Residue "G ARG 346": "NH1" <-> "NH2" Residue "G ARG 408": "NH1" <-> "NH2" Residue "G ARG 454": "NH1" <-> "NH2" Residue "G ARG 457": "NH1" <-> "NH2" Residue "G ARG 466": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29429 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 8014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8014 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 971} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "C" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 805 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 7978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 7978 Classifications: {'peptide': 1025} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "E" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1698 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 11, 'TRANS': 214} Chain: "F" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1577 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 16, 'TRANS': 193} Chain: "G" Number of atoms: 8050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8050 Classifications: {'peptide': 1033} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 58, 'TRANS': 974} Chain breaks: 7 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 14.13, per 1000 atoms: 0.48 Number of scatterers: 29429 At special positions: 0 Unit cell: (152.152, 147.896, 223.44, 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 125 16.00 O 5644 8.00 N 4886 7.00 C 18774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.08 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 538 " - pdb=" SG CYS D 590 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.03 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 209 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.03 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 195 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.03 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.04 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.03 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.03 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A 717 " " NAG A1305 " - " ASN A 801 " " NAG A1306 " - " ASN A1098 " " NAG A1307 " - " ASN A1134 " " NAG D1301 " - " ASN D 234 " " NAG D1302 " - " ASN D 282 " " NAG D1303 " - " ASN D 331 " " NAG D1304 " - " ASN D 616 " " NAG D1305 " - " ASN D 709 " " NAG D1306 " - " ASN D 717 " " NAG D1307 " - " ASN D 801 " " NAG D1308 " - " ASN D1098 " " NAG D1309 " - " ASN D1134 " " NAG G1301 " - " ASN G 282 " " NAG G1302 " - " ASN G 331 " " NAG G1303 " - " ASN G 616 " " NAG G1304 " - " ASN G 709 " " NAG G1305 " - " ASN G 717 " " NAG G1306 " - " ASN G 801 " " NAG G1307 " - " ASN G1098 " " NAG G1308 " - " ASN G1134 " Time building additional restraints: 11.77 Conformation dependent library (CDL) restraints added in 5.9 seconds 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7016 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 62 sheets defined 18.1% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.61 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.901A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 removed outlier: 4.073A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.773A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 390' Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.526A pdb=" N HIS A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.668A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 781 removed outlier: 4.329A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 848 through 853 Processing helix chain 'A' and resid 866 through 882 removed outlier: 3.598A pdb=" N ALA A 879 " --> pdb=" O SER A 875 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 3.794A pdb=" N ALA A 903 " --> pdb=" O PRO A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.883A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 4.211A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 982 removed outlier: 3.501A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 982' Processing helix chain 'A' and resid 985 through 990 removed outlier: 3.901A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1032 removed outlier: 3.815A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.063A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 4.184A pdb=" N THR B 91 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 removed outlier: 3.681A pdb=" N GLU C 82 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 366 through 370 removed outlier: 3.863A pdb=" N TYR D 369 " --> pdb=" O SER D 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.543A pdb=" N ASP D 389 " --> pdb=" O LYS D 386 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 386 through 390' Processing helix chain 'D' and resid 502 through 506 removed outlier: 3.542A pdb=" N HIS D 505 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 737 through 742 Processing helix chain 'D' and resid 747 through 755 removed outlier: 3.703A pdb=" N ASN D 751 " --> pdb=" O THR D 747 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN D 755 " --> pdb=" O ASN D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 761 through 782 removed outlier: 4.195A pdb=" N THR D 778 " --> pdb=" O GLN D 774 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN D 779 " --> pdb=" O ASP D 775 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 782 " --> pdb=" O THR D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 817 through 826 removed outlier: 4.377A pdb=" N LEU D 821 " --> pdb=" O PRO D 817 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU D 822 " --> pdb=" O ILE D 818 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE D 823 " --> pdb=" O GLU D 819 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN D 824 " --> pdb=" O ASP D 820 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 848 through 853 Processing helix chain 'D' and resid 854 through 857 Processing helix chain 'D' and resid 866 through 877 removed outlier: 3.586A pdb=" N LEU D 877 " --> pdb=" O TYR D 873 " (cutoff:3.500A) Processing helix chain 'D' and resid 886 through 891 removed outlier: 4.187A pdb=" N ALA D 890 " --> pdb=" O TRP D 886 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY D 891 " --> pdb=" O THR D 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 886 through 891' Processing helix chain 'D' and resid 897 through 906 removed outlier: 3.801A pdb=" N ALA D 903 " --> pdb=" O PRO D 899 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR D 904 " --> pdb=" O MET D 900 " (cutoff:3.500A) Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.937A pdb=" N LYS D 933 " --> pdb=" O SER D 929 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER D 939 " --> pdb=" O GLN D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 946 through 964 removed outlier: 3.925A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL D 952 " --> pdb=" O LEU D 948 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN D 960 " --> pdb=" O ALA D 956 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS D 964 " --> pdb=" O ASN D 960 " (cutoff:3.500A) Processing helix chain 'D' and resid 976 through 981 removed outlier: 3.637A pdb=" N ILE D 980 " --> pdb=" O VAL D 976 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N PHE D 981 " --> pdb=" O LEU D 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 976 through 981' Processing helix chain 'D' and resid 988 through 994 removed outlier: 3.700A pdb=" N ASP D 994 " --> pdb=" O GLU D 990 " (cutoff:3.500A) Processing helix chain 'D' and resid 997 through 1028 removed outlier: 3.546A pdb=" N ALA D1020 " --> pdb=" O ALA D1016 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.199A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 82 removed outlier: 3.526A pdb=" N GLU F 82 " --> pdb=" O ALA F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 303 Processing helix chain 'G' and resid 337 through 342 removed outlier: 3.713A pdb=" N VAL G 341 " --> pdb=" O PRO G 337 " (cutoff:3.500A) Processing helix chain 'G' and resid 364 through 368 removed outlier: 3.898A pdb=" N VAL G 367 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU G 368 " --> pdb=" O TYR G 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 364 through 368' Processing helix chain 'G' and resid 403 through 408 removed outlier: 4.225A pdb=" N GLU G 406 " --> pdb=" O ARG G 403 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 407 " --> pdb=" O GLY G 404 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 403 through 408' Processing helix chain 'G' and resid 417 through 422 removed outlier: 4.024A pdb=" N TYR G 421 " --> pdb=" O ASN G 417 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN G 422 " --> pdb=" O ILE G 418 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 417 through 422' Processing helix chain 'G' and resid 445 through 450 removed outlier: 4.641A pdb=" N TYR G 449 " --> pdb=" O SER G 446 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 506 Processing helix chain 'G' and resid 746 through 755 removed outlier: 3.532A pdb=" N LEU G 752 " --> pdb=" O GLU G 748 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU G 754 " --> pdb=" O SER G 750 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLN G 755 " --> pdb=" O ASN G 751 " (cutoff:3.500A) Processing helix chain 'G' and resid 761 through 781 removed outlier: 3.546A pdb=" N VAL G 781 " --> pdb=" O ASN G 777 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 826 removed outlier: 3.516A pdb=" N ASN G 824 " --> pdb=" O ASP G 820 " (cutoff:3.500A) Processing helix chain 'G' and resid 848 through 855 Processing helix chain 'G' and resid 866 through 884 removed outlier: 3.645A pdb=" N LEU G 877 " --> pdb=" O TYR G 873 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 878 " --> pdb=" O THR G 874 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE G 882 " --> pdb=" O LEU G 878 " (cutoff:3.500A) Processing helix chain 'G' and resid 886 through 891 removed outlier: 4.299A pdb=" N ALA G 890 " --> pdb=" O TRP G 886 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY G 891 " --> pdb=" O THR G 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 886 through 891' Processing helix chain 'G' and resid 897 through 906 removed outlier: 3.635A pdb=" N TYR G 904 " --> pdb=" O MET G 900 " (cutoff:3.500A) Processing helix chain 'G' and resid 912 through 916 removed outlier: 3.925A pdb=" N VAL G 915 " --> pdb=" O THR G 912 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU G 916 " --> pdb=" O GLN G 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 912 through 916' Processing helix chain 'G' and resid 919 through 941 removed outlier: 3.554A pdb=" N SER G 929 " --> pdb=" O ASN G 925 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY G 932 " --> pdb=" O ASN G 928 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS G 933 " --> pdb=" O SER G 929 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN G 935 " --> pdb=" O ILE G 931 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASP G 936 " --> pdb=" O GLY G 932 " (cutoff:3.500A) Processing helix chain 'G' and resid 945 through 962 removed outlier: 4.313A pdb=" N VAL G 951 " --> pdb=" O LYS G 947 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N VAL G 952 " --> pdb=" O LEU G 948 " (cutoff:3.500A) Processing helix chain 'G' and resid 963 through 968 removed outlier: 3.717A pdb=" N SER G 968 " --> pdb=" O GLN G 965 " (cutoff:3.500A) Processing helix chain 'G' and resid 976 through 983 Processing helix chain 'G' and resid 985 through 1029 removed outlier: 3.959A pdb=" N VAL G 991 " --> pdb=" O PRO G 987 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP G 994 " --> pdb=" O GLU G 990 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU G 996 " --> pdb=" O GLN G 992 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR G 998 " --> pdb=" O ASP G 994 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY G 999 " --> pdb=" O ARG G 995 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU G1001 " --> pdb=" O ILE G 997 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER G1003 " --> pdb=" O GLY G 999 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU G1017 " --> pdb=" O ILE G1013 " (cutoff:3.500A) Processing helix chain 'G' and resid 1143 through 1147 removed outlier: 4.206A pdb=" N SER G1147 " --> pdb=" O GLU G1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.587A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.434A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 227 removed outlier: 7.065A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.515A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 355 through 357 removed outlier: 3.548A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA8, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AA9, first strand: chain 'A' and resid 565 through 567 removed outlier: 3.913A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 3.571A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.826A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.668A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.839A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB7, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AB8, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.782A pdb=" N THR B 120 " --> pdb=" O TYR B 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR B 94 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 122 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA B 92 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.665A pdb=" N VAL C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 20 through 23 removed outlier: 3.868A pdb=" N ILE C 20 " --> pdb=" O LEU C 72 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 44 through 45 Processing sheet with id=AC3, first strand: chain 'D' and resid 27 through 31 removed outlier: 3.826A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 47 through 55 removed outlier: 4.088A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 84 through 85 removed outlier: 4.075A pdb=" N GLY D 107 " --> pdb=" O ARG D 237 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 89 through 96 removed outlier: 4.124A pdb=" N PHE D 92 " --> pdb=" O PHE D 190 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU D 189 " --> pdb=" O LYS D 204 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 191 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE D 201 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 226 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 128 through 129 Processing sheet with id=AC8, first strand: chain 'D' and resid 311 through 316 removed outlier: 7.300A pdb=" N VAL D 595 " --> pdb=" O THR D 315 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 354 through 357 removed outlier: 4.127A pdb=" N ASN D 354 " --> pdb=" O SER D 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER D 399 " --> pdb=" O ASN D 354 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 397 " --> pdb=" O LYS D 356 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 379 through 380 Processing sheet with id=AD2, first strand: chain 'D' and resid 538 through 543 removed outlier: 3.846A pdb=" N PHE D 543 " --> pdb=" O LEU D 546 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.449A pdb=" N GLU D 654 " --> pdb=" O ALA D 694 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N THR D 696 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER D 691 " --> pdb=" O GLN D 675 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLN D 675 " --> pdb=" O SER D 691 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 712 through 728 removed outlier: 6.693A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL D1068 " --> pdb=" O THR D 719 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N GLY D1059 " --> pdb=" O SER D1055 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER D1055 " --> pdb=" O GLY D1059 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL D1061 " --> pdb=" O PRO D1053 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU D1063 " --> pdb=" O SER D1051 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER D1051 " --> pdb=" O LEU D1063 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 734 through 735 Processing sheet with id=AD6, first strand: chain 'D' and resid 1120 through 1121 Processing sheet with id=AD7, first strand: chain 'D' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AD9, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.757A pdb=" N THR E 120 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N TYR E 94 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL E 122 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA E 92 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 155 through 156 removed outlier: 4.230A pdb=" N SER E 192 " --> pdb=" O PHE E 179 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 164 through 166 removed outlier: 3.969A pdb=" N THR E 164 " --> pdb=" O ASN E 212 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.575A pdb=" N VAL F 12 " --> pdb=" O THR F 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.876A pdb=" N ILE F 20 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 43 through 45 Processing sheet with id=AE6, first strand: chain 'F' and resid 117 through 120 removed outlier: 3.895A pdb=" N PHE F 120 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL F 135 " --> pdb=" O PHE F 120 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 150 through 151 removed outlier: 4.179A pdb=" N LYS F 151 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER F 194 " --> pdb=" O LYS F 151 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 168 through 169 removed outlier: 3.574A pdb=" N ALA F 175 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 28 through 30 Processing sheet with id=AF1, first strand: chain 'G' and resid 36 through 37 removed outlier: 7.454A pdb=" N VAL G 36 " --> pdb=" O LEU G 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'G' and resid 48 through 49 removed outlier: 3.577A pdb=" N VAL G 289 " --> pdb=" O LEU G 276 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 54 through 55 removed outlier: 3.642A pdb=" N PHE G 55 " --> pdb=" O GLN G 271 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 66 through 67 Processing sheet with id=AF5, first strand: chain 'G' and resid 89 through 92 removed outlier: 4.007A pdb=" N GLU G 96 " --> pdb=" O ASN G 186 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 89 through 92 Processing sheet with id=AF7, first strand: chain 'G' and resid 101 through 107 removed outlier: 4.114A pdb=" N GLY G 103 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY G 107 " --> pdb=" O ARG G 237 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 121 through 122 removed outlier: 3.531A pdb=" N ASN G 125 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 311 through 314 Processing sheet with id=AG1, first strand: chain 'G' and resid 354 through 358 removed outlier: 4.120A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER G 399 " --> pdb=" O ASN G 354 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL G 512 " --> pdb=" O ASP G 398 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 375 through 376 removed outlier: 3.510A pdb=" N ALA G 435 " --> pdb=" O THR G 376 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 391 through 392 removed outlier: 3.938A pdb=" N PHE G 392 " --> pdb=" O VAL G 524 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 538 through 543 removed outlier: 3.601A pdb=" N VAL G 539 " --> pdb=" O GLY G 550 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY G 550 " --> pdb=" O VAL G 539 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY G 548 " --> pdb=" O PHE G 541 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR G 553 " --> pdb=" O ASP G 586 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 654 through 655 removed outlier: 6.024A pdb=" N GLU G 654 " --> pdb=" O ALA G 694 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N THR G 696 " --> pdb=" O GLU G 654 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN G 675 " --> pdb=" O SER G 691 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 715 through 728 removed outlier: 6.296A pdb=" N GLU G1072 " --> pdb=" O PRO G 715 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N GLY G1059 " --> pdb=" O SER G1055 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N SER G1055 " --> pdb=" O GLY G1059 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL G1061 " --> pdb=" O PRO G1053 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU G1063 " --> pdb=" O SER G1051 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER G1051 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N VAL G1065 " --> pdb=" O LEU G1049 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 1120 through 1125 removed outlier: 4.674A pdb=" N ALA G1087 " --> pdb=" O SER G1123 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 1094 through 1097 748 hydrogen bonds defined for protein. 1980 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: 12.41 Time building geometry restraints manager: 12.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9289 1.34 - 1.46: 7412 1.46 - 1.59: 13269 1.59 - 1.72: 0 1.72 - 1.84: 154 Bond restraints: 30124 Sorted by residual: bond pdb=" CA ARG G 319 " pdb=" C ARG G 319 " ideal model delta sigma weight residual 1.522 1.469 0.053 1.08e-02 8.57e+03 2.40e+01 bond pdb=" CA PHE G 318 " pdb=" C PHE G 318 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.30e-02 5.92e+03 1.99e+01 bond pdb=" CA CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sigma weight residual 1.524 1.584 -0.060 1.62e-02 3.81e+03 1.39e+01 bond pdb=" CA ASP D 985 " pdb=" C ASP D 985 " ideal model delta sigma weight residual 1.524 1.480 0.043 1.26e-02 6.30e+03 1.18e+01 bond pdb=" N ARG G 319 " pdb=" CA ARG G 319 " ideal model delta sigma weight residual 1.461 1.420 0.041 1.19e-02 7.06e+03 1.18e+01 ... (remaining 30119 not shown) Histogram of bond angle deviations from ideal: 97.68 - 104.95: 591 104.95 - 112.22: 15072 112.22 - 119.48: 9088 119.48 - 126.75: 15925 126.75 - 134.02: 353 Bond angle restraints: 41029 Sorted by residual: angle pdb=" N PRO D 986 " pdb=" CA PRO D 986 " pdb=" C PRO D 986 " ideal model delta sigma weight residual 110.70 123.99 -13.29 1.22e+00 6.72e-01 1.19e+02 angle pdb=" N GLN G 134 " pdb=" CA GLN G 134 " pdb=" C GLN G 134 " ideal model delta sigma weight residual 113.19 101.76 11.43 1.58e+00 4.01e-01 5.23e+01 angle pdb=" N VAL A 991 " pdb=" CA VAL A 991 " pdb=" C VAL A 991 " ideal model delta sigma weight residual 113.71 106.99 6.72 9.50e-01 1.11e+00 5.00e+01 angle pdb=" C ASP D 985 " pdb=" N PRO D 986 " pdb=" CA PRO D 986 " ideal model delta sigma weight residual 120.38 113.36 7.02 1.03e+00 9.43e-01 4.64e+01 angle pdb=" N GLU D 988 " pdb=" CA GLU D 988 " pdb=" C GLU D 988 " ideal model delta sigma weight residual 113.50 105.88 7.62 1.23e+00 6.61e-01 3.84e+01 ... (remaining 41024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 17295 17.94 - 35.88: 776 35.88 - 53.81: 142 53.81 - 71.75: 26 71.75 - 89.69: 12 Dihedral angle restraints: 18251 sinusoidal: 7336 harmonic: 10915 Sorted by residual: dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual -86.00 -40.70 -45.30 1 1.00e+01 1.00e-02 2.85e+01 dihedral pdb=" CA ASN D 99 " pdb=" C ASN D 99 " pdb=" N ILE D 100 " pdb=" CA ILE D 100 " ideal model delta harmonic sigma weight residual 180.00 -157.99 -22.01 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA ARG F 191 " pdb=" C ARG F 191 " pdb=" N SER F 192 " pdb=" CA SER F 192 " ideal model delta harmonic sigma weight residual 180.00 160.91 19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 18248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 4692 0.154 - 0.308: 16 0.308 - 0.463: 1 0.463 - 0.617: 2 0.617 - 0.771: 1 Chirality restraints: 4712 Sorted by residual: chirality pdb=" C1 NAG G1301 " pdb=" ND2 ASN G 282 " pdb=" C2 NAG G1301 " pdb=" O5 NAG G1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.49e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.69e+00 chirality pdb=" CA PRO D 986 " pdb=" N PRO D 986 " pdb=" C PRO D 986 " pdb=" CB PRO D 986 " both_signs ideal model delta sigma weight residual False 2.72 2.24 0.47 2.00e-01 2.50e+01 5.62e+00 ... (remaining 4709 not shown) Planarity restraints: 5309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " -0.354 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C7 NAG A1301 " 0.087 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " -0.146 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " 0.539 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1302 " 0.305 2.00e-02 2.50e+03 2.58e-01 8.31e+02 pdb=" C7 NAG D1302 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D1302 " 0.185 2.00e-02 2.50e+03 pdb=" N2 NAG D1302 " -0.445 2.00e-02 2.50e+03 pdb=" O7 NAG D1302 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D1305 " 0.304 2.00e-02 2.50e+03 2.56e-01 8.16e+02 pdb=" C7 NAG D1305 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG D1305 " 0.191 2.00e-02 2.50e+03 pdb=" N2 NAG D1305 " -0.436 2.00e-02 2.50e+03 pdb=" O7 NAG D1305 " 0.023 2.00e-02 2.50e+03 ... (remaining 5306 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3133 2.75 - 3.29: 28938 3.29 - 3.83: 48557 3.83 - 4.36: 56436 4.36 - 4.90: 96591 Nonbonded interactions: 233655 Sorted by model distance: nonbonded pdb=" OG1 THR A 470 " pdb=" OE1 GLN B 82 " model vdw 2.216 2.440 nonbonded pdb=" OG1 THR D 470 " pdb=" OE1 GLN E 82 " model vdw 2.220 2.440 nonbonded pdb=" OE1 GLN G 52 " pdb=" OG1 THR G 274 " model vdw 2.235 2.440 nonbonded pdb=" O GLY A 880 " pdb=" OG SER A 884 " model vdw 2.239 2.440 nonbonded pdb=" OG SER C 31 " pdb=" OD1 ASP C 49 " model vdw 2.240 2.440 ... (remaining 233650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 243 or resid 262 through 1147 or resid 1301 thr \ ough 1307)) selection = (chain 'D' and (resid 26 through 1147 or resid 1301 through 1307)) selection = (chain 'G' and (resid 26 through 68 or resid 80 through 243 or resid 262 through \ 1147 or resid 1301 through 1307)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.010 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 8.370 Check model and map are aligned: 0.420 Set scattering table: 0.290 Process input model: 77.270 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30124 Z= 0.219 Angle : 0.701 13.292 41029 Z= 0.440 Chirality : 0.046 0.771 4712 Planarity : 0.011 0.303 5285 Dihedral : 10.315 89.691 11100 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.14 % Favored : 91.65 % Rotamer: Outliers : 6.82 % Allowed : 8.65 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.11), residues: 3700 helix: -3.29 (0.13), residues: 619 sheet: -2.55 (0.16), residues: 894 loop : -3.83 (0.10), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 64 HIS 0.002 0.000 HIS E 213 PHE 0.023 0.001 PHE G 318 TYR 0.007 0.001 TYR G 202 ARG 0.002 0.000 ARG G 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 711 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 VAL cc_start: 0.8370 (m) cc_final: 0.8006 (p) REVERT: A 105 ILE cc_start: 0.8071 (mt) cc_final: 0.7748 (mp) REVERT: A 132 GLU cc_start: 0.7303 (mp0) cc_final: 0.7064 (mp0) REVERT: A 168 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.6854 (m-80) REVERT: A 188 ARG cc_start: 0.7111 (ptp90) cc_final: 0.6868 (ptp90) REVERT: A 200 LYS cc_start: 0.7587 (mttm) cc_final: 0.7340 (mttm) REVERT: A 269 TYR cc_start: 0.7917 (m-80) cc_final: 0.7641 (m-80) REVERT: A 316 SER cc_start: 0.7898 (t) cc_final: 0.7514 (p) REVERT: A 325 SER cc_start: 0.8032 (OUTLIER) cc_final: 0.7669 (m) REVERT: A 532 ASN cc_start: 0.7162 (t0) cc_final: 0.6788 (t0) REVERT: A 537 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7631 (ttpp) REVERT: A 603 ASN cc_start: 0.7570 (t0) cc_final: 0.7369 (t0) REVERT: A 675 GLN cc_start: 0.6425 (mm-40) cc_final: 0.6165 (mm-40) REVERT: A 733 LYS cc_start: 0.8129 (mtmt) cc_final: 0.7809 (mtmt) REVERT: A 736 VAL cc_start: 0.8569 (m) cc_final: 0.8246 (t) REVERT: A 737 ASP cc_start: 0.6628 (t0) cc_final: 0.6418 (t70) REVERT: A 776 LYS cc_start: 0.7826 (ttpt) cc_final: 0.7479 (ttpt) REVERT: A 823 PHE cc_start: 0.7324 (m-80) cc_final: 0.7076 (m-80) REVERT: A 849 LEU cc_start: 0.8076 (tp) cc_final: 0.7873 (tp) REVERT: A 878 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8324 (tp) REVERT: A 922 LEU cc_start: 0.8227 (tp) cc_final: 0.7982 (tt) REVERT: A 934 ILE cc_start: 0.7910 (mt) cc_final: 0.7695 (mm) REVERT: A 947 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7496 (mtmm) REVERT: A 949 GLN cc_start: 0.6988 (mm110) cc_final: 0.6761 (mm-40) REVERT: A 969 LYS cc_start: 0.7931 (OUTLIER) cc_final: 0.7466 (pptt) REVERT: A 979 ASP cc_start: 0.6392 (m-30) cc_final: 0.6173 (t0) REVERT: A 1017 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6654 (tm-30) REVERT: A 1028 LYS cc_start: 0.8361 (mttm) cc_final: 0.8053 (mttm) REVERT: A 1144 GLU cc_start: 0.6853 (tp30) cc_final: 0.6292 (tp30) REVERT: D 54 LEU cc_start: 0.7606 (mm) cc_final: 0.7054 (mt) REVERT: D 105 ILE cc_start: 0.7878 (mt) cc_final: 0.7555 (mt) REVERT: D 126 VAL cc_start: 0.6926 (t) cc_final: 0.6702 (m) REVERT: D 188 ARG cc_start: 0.7247 (mtt-85) cc_final: 0.6874 (mtt-85) REVERT: D 189 GLU cc_start: 0.6803 (mm-30) cc_final: 0.6524 (mm-30) REVERT: D 206 THR cc_start: 0.8291 (t) cc_final: 0.7915 (t) REVERT: D 239 GLN cc_start: 0.6596 (tp40) cc_final: 0.6394 (tm-30) REVERT: D 307 THR cc_start: 0.8387 (m) cc_final: 0.8177 (p) REVERT: D 346 ARG cc_start: 0.7393 (mtt-85) cc_final: 0.6836 (mtt-85) REVERT: D 365 TYR cc_start: 0.6760 (m-80) cc_final: 0.6515 (m-80) REVERT: D 380 TYR cc_start: 0.6074 (m-80) cc_final: 0.5830 (m-80) REVERT: D 393 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7745 (p) REVERT: D 513 LEU cc_start: 0.7157 (mt) cc_final: 0.6935 (mt) REVERT: D 523 THR cc_start: 0.5854 (OUTLIER) cc_final: 0.5627 (p) REVERT: D 551 VAL cc_start: 0.8119 (t) cc_final: 0.7800 (m) REVERT: D 692 ILE cc_start: 0.8184 (mm) cc_final: 0.7684 (mt) REVERT: D 705 VAL cc_start: 0.8426 (t) cc_final: 0.8185 (p) REVERT: D 755 GLN cc_start: 0.7478 (mm-40) cc_final: 0.7156 (mm-40) REVERT: D 854 LYS cc_start: 0.8379 (ttmm) cc_final: 0.8034 (ttpp) REVERT: D 878 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8364 (tt) REVERT: D 886 TRP cc_start: 0.8416 (p90) cc_final: 0.8003 (p90) REVERT: D 921 LYS cc_start: 0.7859 (tptp) cc_final: 0.7658 (tptp) REVERT: D 945 LEU cc_start: 0.7899 (mm) cc_final: 0.7600 (mp) REVERT: D 969 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7975 (pttt) REVERT: D 1017 GLU cc_start: 0.6994 (tm-30) cc_final: 0.6702 (tm-30) REVERT: D 1029 MET cc_start: 0.7706 (ttm) cc_final: 0.7453 (ttm) REVERT: D 1066 THR cc_start: 0.7814 (p) cc_final: 0.7560 (p) REVERT: D 1086 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7611 (pttm) REVERT: D 1118 ASP cc_start: 0.6538 (t0) cc_final: 0.6221 (t0) REVERT: D 1139 ASP cc_start: 0.7438 (p0) cc_final: 0.7230 (p0) REVERT: E 156 LYS cc_start: -0.1056 (OUTLIER) cc_final: -0.2091 (ttmp) REVERT: F 200 GLU cc_start: 0.0797 (OUTLIER) cc_final: 0.0147 (pm20) REVERT: G 28 TYR cc_start: 0.7786 (m-80) cc_final: 0.7520 (m-10) REVERT: G 53 ASP cc_start: 0.6028 (t0) cc_final: 0.5623 (t0) REVERT: G 99 ASN cc_start: 0.7689 (m-40) cc_final: 0.7429 (m-40) REVERT: G 129 LYS cc_start: 0.7567 (ttmm) cc_final: 0.7138 (mtmt) REVERT: G 136 CYS cc_start: 0.3102 (OUTLIER) cc_final: 0.2775 (p) REVERT: G 186 ASN cc_start: 0.7233 (p0) cc_final: 0.6559 (p0) REVERT: G 187 LEU cc_start: 0.7600 (tp) cc_final: 0.7209 (tp) REVERT: G 189 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6065 (mm-30) REVERT: G 269 TYR cc_start: 0.7588 (m-80) cc_final: 0.7239 (m-80) REVERT: G 327 VAL cc_start: 0.8409 (t) cc_final: 0.8110 (p) REVERT: G 364 ASP cc_start: 0.7313 (t70) cc_final: 0.6962 (t70) REVERT: G 422 ASN cc_start: 0.7398 (m-40) cc_final: 0.6672 (m-40) REVERT: G 444 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6441 (tppt) REVERT: G 453 TYR cc_start: 0.5322 (t80) cc_final: 0.4869 (t80) REVERT: G 493 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.6034 (mmp-170) REVERT: G 546 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7540 (tt) REVERT: G 574 ASP cc_start: 0.7000 (t0) cc_final: 0.6768 (t0) REVERT: G 576 VAL cc_start: 0.8700 (p) cc_final: 0.8386 (t) REVERT: G 655 TYR cc_start: 0.8267 (t80) cc_final: 0.7845 (t80) REVERT: G 663 ASP cc_start: 0.6948 (t70) cc_final: 0.6557 (t70) REVERT: G 673 SER cc_start: 0.8668 (p) cc_final: 0.8292 (m) REVERT: G 711 SER cc_start: 0.8113 (m) cc_final: 0.7877 (p) REVERT: G 718 PHE cc_start: 0.7541 (p90) cc_final: 0.6991 (p90) REVERT: G 725 GLU cc_start: 0.6915 (tt0) cc_final: 0.6411 (tt0) REVERT: G 727 LEU cc_start: 0.7835 (mt) cc_final: 0.7563 (mt) REVERT: G 764 LYS cc_start: 0.8296 (tttt) cc_final: 0.8076 (ttmm) REVERT: G 776 LYS cc_start: 0.7500 (ttpt) cc_final: 0.7172 (ttpt) REVERT: G 790 LYS cc_start: 0.7557 (mtmm) cc_final: 0.7294 (mtmm) REVERT: G 821 LEU cc_start: 0.7902 (tt) cc_final: 0.7497 (mp) REVERT: G 855 PHE cc_start: 0.8121 (m-10) cc_final: 0.7902 (m-80) REVERT: G 921 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7732 (mmmm) REVERT: G 976 VAL cc_start: 0.8549 (t) cc_final: 0.8268 (m) REVERT: G 993 ILE cc_start: 0.8702 (tp) cc_final: 0.8492 (mm) REVERT: G 1028 LYS cc_start: 0.7637 (mttm) cc_final: 0.7409 (mttt) REVERT: G 1111 GLU cc_start: 0.7094 (tt0) cc_final: 0.6784 (tt0) REVERT: G 1118 ASP cc_start: 0.6666 (t70) cc_final: 0.6429 (t70) REVERT: G 1125 ASN cc_start: 0.7379 (p0) cc_final: 0.7117 (p0) REVERT: G 1136 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7767 (p) outliers start: 219 outliers final: 92 residues processed: 881 average time/residue: 0.4337 time to fit residues: 589.1431 Evaluate side-chains 661 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 550 time to evaluate : 3.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 537 LYS Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 96 GLU Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 538 CYS Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 590 CYS Chi-restraints excluded: chain D residue 873 TYR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1086 LYS Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain E residue 205 GLN Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 194 ASN Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 361 CYS Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 444 LYS Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 546 LEU Chi-restraints excluded: chain G residue 825 LYS Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1136 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 0.9990 chunk 282 optimal weight: 6.9990 chunk 156 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 190 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 292 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 177 optimal weight: 0.5980 chunk 217 optimal weight: 2.9990 chunk 338 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 ASN A 218 GLN A 388 ASN A 414 GLN A 448 ASN A 762 GLN A 774 GLN A 784 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 955 ASN A1010 GLN A1011 GLN A1048 HIS B 39 GLN B 118 GLN C 6 GLN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 88 GLN D 115 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN D 218 GLN D 317 ASN D 414 GLN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 450 ASN D 540 ASN D 564 GLN D 580 GLN D 762 GLN ** D 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 804 GLN D 853 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 919 ASN ** D 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 978 ASN D1005 GLN D1011 GLN D1048 HIS D1119 ASN D1125 ASN E 39 GLN E 54 ASN E 118 GLN E 205 GLN F 6 GLN F 37 GLN F 88 GLN F 110 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 HIS F 196 GLN G 81 ASN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN G 186 ASN G 239 GLN ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 409 GLN ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 481 ASN ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 540 ASN G 542 ASN G 563 GLN G 641 ASN G 690 GLN G 784 GLN G 853 GLN ** G 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 GLN ** G 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 919 ASN G 960 ASN G 965 GLN ** G1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1010 GLN G1011 GLN G1048 HIS Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 30124 Z= 0.239 Angle : 0.570 8.289 41029 Z= 0.295 Chirality : 0.045 0.350 4712 Planarity : 0.005 0.088 5285 Dihedral : 7.628 80.118 4800 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.19 % Favored : 91.76 % Rotamer: Outliers : 6.32 % Allowed : 13.51 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.12), residues: 3700 helix: -1.38 (0.19), residues: 636 sheet: -2.02 (0.16), residues: 851 loop : -3.30 (0.11), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 53 HIS 0.004 0.001 HIS A 66 PHE 0.030 0.002 PHE A 133 TYR 0.024 0.001 TYR D1067 ARG 0.007 0.000 ARG G1107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 561 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.7655 (m-80) cc_final: 0.7361 (m-80) REVERT: A 101 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.6950 (tp) REVERT: A 104 TRP cc_start: 0.8174 (m-90) cc_final: 0.7424 (m-90) REVERT: A 105 ILE cc_start: 0.7944 (mt) cc_final: 0.7743 (mm) REVERT: A 127 VAL cc_start: 0.7615 (OUTLIER) cc_final: 0.7373 (p) REVERT: A 168 PHE cc_start: 0.7979 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: A 200 LYS cc_start: 0.7881 (mttm) cc_final: 0.7621 (mttp) REVERT: A 269 TYR cc_start: 0.7853 (m-80) cc_final: 0.7523 (m-80) REVERT: A 316 SER cc_start: 0.8073 (t) cc_final: 0.7840 (p) REVERT: A 324 GLU cc_start: 0.6383 (OUTLIER) cc_final: 0.6104 (tm-30) REVERT: A 325 SER cc_start: 0.8050 (m) cc_final: 0.7157 (m) REVERT: A 532 ASN cc_start: 0.7402 (t0) cc_final: 0.6974 (t0) REVERT: A 675 GLN cc_start: 0.6574 (mm-40) cc_final: 0.6306 (mm-40) REVERT: A 776 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7474 (ttpt) REVERT: A 823 PHE cc_start: 0.7433 (m-80) cc_final: 0.7203 (m-80) REVERT: A 851 CYS cc_start: 0.7666 (t) cc_final: 0.7374 (t) REVERT: A 902 MET cc_start: 0.7771 (mmm) cc_final: 0.7480 (tpt) REVERT: A 917 TYR cc_start: 0.7982 (m-80) cc_final: 0.7730 (m-10) REVERT: A 949 GLN cc_start: 0.7622 (mm110) cc_final: 0.7301 (mm-40) REVERT: A 969 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7557 (pptt) REVERT: A 1017 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6725 (tm-30) REVERT: A 1097 SER cc_start: 0.8498 (t) cc_final: 0.8244 (p) REVERT: A 1144 GLU cc_start: 0.7078 (tp30) cc_final: 0.6572 (tp30) REVERT: D 66 HIS cc_start: 0.7563 (m-70) cc_final: 0.7268 (m-70) REVERT: D 105 ILE cc_start: 0.7984 (mt) cc_final: 0.7634 (mt) REVERT: D 126 VAL cc_start: 0.7144 (t) cc_final: 0.6929 (m) REVERT: D 141 LEU cc_start: 0.5112 (OUTLIER) cc_final: 0.4688 (mt) REVERT: D 206 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7611 (t) REVERT: D 319 ARG cc_start: 0.7399 (ttm170) cc_final: 0.7058 (ttm-80) REVERT: D 346 ARG cc_start: 0.7450 (mtt-85) cc_final: 0.7203 (mtt-85) REVERT: D 692 ILE cc_start: 0.8108 (mm) cc_final: 0.7822 (mt) REVERT: D 705 VAL cc_start: 0.8596 (t) cc_final: 0.8308 (p) REVERT: D 735 SER cc_start: 0.8153 (p) cc_final: 0.7917 (t) REVERT: D 737 ASP cc_start: 0.6645 (t70) cc_final: 0.6300 (t0) REVERT: D 759 PHE cc_start: 0.6329 (m-80) cc_final: 0.5943 (m-80) REVERT: D 804 GLN cc_start: 0.7691 (mt0) cc_final: 0.7247 (mm-40) REVERT: D 816 SER cc_start: 0.8413 (p) cc_final: 0.8075 (t) REVERT: D 859 THR cc_start: 0.7879 (p) cc_final: 0.7645 (m) REVERT: D 960 ASN cc_start: 0.7886 (m110) cc_final: 0.7645 (m-40) REVERT: D 969 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8190 (pttm) REVERT: D 978 ASN cc_start: 0.7810 (m-40) cc_final: 0.7429 (m110) REVERT: D 988 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: D 992 GLN cc_start: 0.7220 (mt0) cc_final: 0.6929 (mt0) REVERT: D 1019 ARG cc_start: 0.7539 (ttp80) cc_final: 0.7300 (ttp-110) REVERT: D 1029 MET cc_start: 0.7856 (ttm) cc_final: 0.7508 (ttm) REVERT: D 1112 PRO cc_start: 0.8142 (Cg_exo) cc_final: 0.7907 (Cg_endo) REVERT: D 1118 ASP cc_start: 0.6777 (t0) cc_final: 0.6379 (t0) REVERT: F 200 GLU cc_start: 0.0753 (OUTLIER) cc_final: 0.0090 (pm20) REVERT: G 47 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8417 (t) REVERT: G 117 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6602 (mt) REVERT: G 129 LYS cc_start: 0.7726 (ttmm) cc_final: 0.7506 (ptpt) REVERT: G 130 VAL cc_start: 0.7129 (t) cc_final: 0.6838 (p) REVERT: G 186 ASN cc_start: 0.7164 (p0) cc_final: 0.6669 (p0) REVERT: G 327 VAL cc_start: 0.8452 (t) cc_final: 0.8132 (p) REVERT: G 364 ASP cc_start: 0.7285 (t70) cc_final: 0.6919 (t70) REVERT: G 378 LYS cc_start: 0.7290 (tptm) cc_final: 0.6943 (tptm) REVERT: G 453 TYR cc_start: 0.5472 (t80) cc_final: 0.5177 (t80) REVERT: G 493 ARG cc_start: 0.6763 (OUTLIER) cc_final: 0.6212 (mmp-170) REVERT: G 546 LEU cc_start: 0.7717 (tm) cc_final: 0.7455 (tt) REVERT: G 574 ASP cc_start: 0.7083 (t0) cc_final: 0.6794 (t0) REVERT: G 586 ASP cc_start: 0.7132 (t0) cc_final: 0.6671 (t0) REVERT: G 673 SER cc_start: 0.8487 (p) cc_final: 0.8257 (m) REVERT: G 675 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6915 (mm-40) REVERT: G 750 SER cc_start: 0.8470 (m) cc_final: 0.8214 (p) REVERT: G 764 LYS cc_start: 0.7897 (tttt) cc_final: 0.7563 (ttmm) REVERT: G 775 ASP cc_start: 0.7423 (m-30) cc_final: 0.7038 (m-30) REVERT: G 776 LYS cc_start: 0.7747 (ttpt) cc_final: 0.7522 (ttpt) REVERT: G 819 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7089 (mt-10) REVERT: G 821 LEU cc_start: 0.7889 (tt) cc_final: 0.7285 (mp) REVERT: G 853 GLN cc_start: 0.7879 (mt0) cc_final: 0.7642 (mt0) REVERT: G 856 LYS cc_start: 0.8470 (mmtp) cc_final: 0.8257 (mppt) REVERT: G 884 SER cc_start: 0.8208 (t) cc_final: 0.7992 (p) REVERT: G 949 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7643 (mm-40) REVERT: G 977 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7485 (mm) REVERT: G 993 ILE cc_start: 0.8399 (tp) cc_final: 0.8078 (tt) REVERT: G 998 THR cc_start: 0.8473 (t) cc_final: 0.8147 (p) REVERT: G 1017 GLU cc_start: 0.6949 (tm-30) cc_final: 0.6638 (tm-30) REVERT: G 1019 ARG cc_start: 0.7443 (ttp-110) cc_final: 0.7224 (ttp80) REVERT: G 1097 SER cc_start: 0.8397 (t) cc_final: 0.8181 (p) REVERT: G 1118 ASP cc_start: 0.6975 (t70) cc_final: 0.6662 (t70) REVERT: G 1125 ASN cc_start: 0.7650 (p0) cc_final: 0.7285 (p0) REVERT: G 1136 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.7861 (p) outliers start: 203 outliers final: 123 residues processed: 719 average time/residue: 0.4255 time to fit residues: 478.0730 Evaluate side-chains 665 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 527 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 1014 ARG Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 206 THR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1073 LYS Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1127 ASP Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 317 ASN Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 542 ASN Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 746 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 977 LEU Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1136 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 0.9980 chunk 105 optimal weight: 40.0000 chunk 281 optimal weight: 0.3980 chunk 230 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 339 optimal weight: 2.9990 chunk 366 optimal weight: 0.8980 chunk 302 optimal weight: 0.0980 chunk 336 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 272 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN D 194 ASN ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 774 GLN D 804 GLN D 872 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 935 GLN ** D 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1125 ASN F 110 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 HIS ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30124 Z= 0.189 Angle : 0.533 8.248 41029 Z= 0.275 Chirality : 0.044 0.249 4712 Planarity : 0.005 0.097 5285 Dihedral : 7.053 79.030 4754 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.46 % Favored : 91.49 % Rotamer: Outliers : 6.01 % Allowed : 15.19 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.13), residues: 3700 helix: -0.64 (0.21), residues: 637 sheet: -1.80 (0.16), residues: 867 loop : -3.06 (0.11), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 64 HIS 0.005 0.001 HIS F 190 PHE 0.022 0.001 PHE D 135 TYR 0.020 0.001 TYR D1067 ARG 0.006 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 529 time to evaluate : 3.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7187 (mp) REVERT: A 102 ARG cc_start: 0.7119 (mtm-85) cc_final: 0.6901 (mtp85) REVERT: A 104 TRP cc_start: 0.8236 (m-90) cc_final: 0.7618 (m-90) REVERT: A 105 ILE cc_start: 0.7986 (mt) cc_final: 0.7743 (mm) REVERT: A 127 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7516 (p) REVERT: A 133 PHE cc_start: 0.8341 (m-80) cc_final: 0.8126 (m-80) REVERT: A 168 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.7347 (m-80) REVERT: A 200 LYS cc_start: 0.7847 (mttm) cc_final: 0.7580 (mttp) REVERT: A 231 ILE cc_start: 0.8160 (mt) cc_final: 0.7883 (tt) REVERT: A 316 SER cc_start: 0.8043 (t) cc_final: 0.7798 (p) REVERT: A 324 GLU cc_start: 0.6359 (tt0) cc_final: 0.6068 (tm-30) REVERT: A 325 SER cc_start: 0.8115 (m) cc_final: 0.7224 (m) REVERT: A 517 LEU cc_start: 0.3275 (OUTLIER) cc_final: 0.2893 (tm) REVERT: A 532 ASN cc_start: 0.7495 (t0) cc_final: 0.7048 (t0) REVERT: A 675 GLN cc_start: 0.6541 (mm-40) cc_final: 0.6267 (mm-40) REVERT: A 776 LYS cc_start: 0.7850 (ttpt) cc_final: 0.7489 (ttpt) REVERT: A 795 LYS cc_start: 0.7830 (mptm) cc_final: 0.7560 (mptt) REVERT: A 851 CYS cc_start: 0.7638 (t) cc_final: 0.7415 (t) REVERT: A 868 GLU cc_start: 0.6803 (tp30) cc_final: 0.6504 (tp30) REVERT: A 902 MET cc_start: 0.7775 (mmm) cc_final: 0.7476 (tpt) REVERT: A 947 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7984 (mtpp) REVERT: A 949 GLN cc_start: 0.7661 (mm110) cc_final: 0.7345 (mm-40) REVERT: A 960 ASN cc_start: 0.7781 (t0) cc_final: 0.7495 (t0) REVERT: A 969 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7547 (pptt) REVERT: A 1017 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6686 (tm-30) REVERT: A 1097 SER cc_start: 0.8490 (t) cc_final: 0.8248 (p) REVERT: D 83 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7298 (p) REVERT: D 105 ILE cc_start: 0.7875 (mt) cc_final: 0.7502 (mt) REVERT: D 188 ARG cc_start: 0.7478 (mtt-85) cc_final: 0.6996 (mtt-85) REVERT: D 239 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6717 (tm-30) REVERT: D 317 ASN cc_start: 0.7255 (m-40) cc_final: 0.6894 (m-40) REVERT: D 319 ARG cc_start: 0.7391 (ttm170) cc_final: 0.7055 (ttm-80) REVERT: D 346 ARG cc_start: 0.7430 (mtt-85) cc_final: 0.7229 (mtt-85) REVERT: D 599 THR cc_start: 0.8073 (m) cc_final: 0.7810 (p) REVERT: D 705 VAL cc_start: 0.8617 (t) cc_final: 0.8335 (p) REVERT: D 808 ASP cc_start: 0.7078 (t0) cc_final: 0.6577 (p0) REVERT: D 816 SER cc_start: 0.8399 (p) cc_final: 0.8144 (t) REVERT: D 854 LYS cc_start: 0.8373 (ttmm) cc_final: 0.8048 (ttpp) REVERT: D 960 ASN cc_start: 0.7882 (m110) cc_final: 0.7626 (m-40) REVERT: D 969 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8120 (pttm) REVERT: D 978 ASN cc_start: 0.7879 (m-40) cc_final: 0.7572 (m-40) REVERT: D 988 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6427 (tm-30) REVERT: D 992 GLN cc_start: 0.7187 (mt0) cc_final: 0.6928 (mt0) REVERT: D 1005 GLN cc_start: 0.7343 (tt0) cc_final: 0.7113 (tt0) REVERT: D 1029 MET cc_start: 0.7715 (ttm) cc_final: 0.7461 (ttm) REVERT: D 1112 PRO cc_start: 0.8216 (Cg_exo) cc_final: 0.7996 (Cg_endo) REVERT: D 1118 ASP cc_start: 0.6813 (t0) cc_final: 0.6412 (t0) REVERT: F 200 GLU cc_start: 0.0652 (OUTLIER) cc_final: 0.0116 (pm20) REVERT: G 47 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8403 (t) REVERT: G 63 THR cc_start: 0.7793 (OUTLIER) cc_final: 0.6839 (t) REVERT: G 117 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6364 (mt) REVERT: G 129 LYS cc_start: 0.7719 (ttmm) cc_final: 0.7434 (ptpt) REVERT: G 130 VAL cc_start: 0.7146 (t) cc_final: 0.6815 (p) REVERT: G 186 ASN cc_start: 0.7264 (p0) cc_final: 0.6741 (p0) REVERT: G 190 PHE cc_start: 0.8014 (m-80) cc_final: 0.7475 (m-80) REVERT: G 364 ASP cc_start: 0.7266 (t70) cc_final: 0.6886 (t70) REVERT: G 380 TYR cc_start: 0.7814 (m-10) cc_final: 0.7037 (m-10) REVERT: G 453 TYR cc_start: 0.5506 (t80) cc_final: 0.5190 (t80) REVERT: G 493 ARG cc_start: 0.6715 (OUTLIER) cc_final: 0.6286 (mmp-170) REVERT: G 546 LEU cc_start: 0.7726 (tm) cc_final: 0.7481 (tt) REVERT: G 574 ASP cc_start: 0.7070 (t0) cc_final: 0.6783 (t0) REVERT: G 586 ASP cc_start: 0.7116 (t0) cc_final: 0.6647 (t0) REVERT: G 599 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8266 (p) REVERT: G 673 SER cc_start: 0.8538 (p) cc_final: 0.8334 (t) REVERT: G 675 GLN cc_start: 0.7180 (mm-40) cc_final: 0.6907 (mm-40) REVERT: G 750 SER cc_start: 0.8488 (m) cc_final: 0.8232 (p) REVERT: G 764 LYS cc_start: 0.7927 (tttt) cc_final: 0.7646 (ttmm) REVERT: G 775 ASP cc_start: 0.7450 (m-30) cc_final: 0.7066 (m-30) REVERT: G 776 LYS cc_start: 0.7711 (ttpt) cc_final: 0.7497 (ttpt) REVERT: G 821 LEU cc_start: 0.7939 (tt) cc_final: 0.7610 (tp) REVERT: G 853 GLN cc_start: 0.7854 (mt0) cc_final: 0.7587 (mt0) REVERT: G 855 PHE cc_start: 0.8025 (m-10) cc_final: 0.7748 (m-10) REVERT: G 884 SER cc_start: 0.8228 (t) cc_final: 0.7981 (p) REVERT: G 949 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7525 (mm-40) REVERT: G 993 ILE cc_start: 0.8331 (tp) cc_final: 0.8099 (tt) REVERT: G 998 THR cc_start: 0.8279 (t) cc_final: 0.8032 (p) REVERT: G 1017 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6681 (tm-30) REVERT: G 1019 ARG cc_start: 0.7411 (ttp-110) cc_final: 0.7205 (ttp80) REVERT: G 1072 GLU cc_start: 0.7810 (pm20) cc_final: 0.7471 (pm20) REVERT: G 1107 ARG cc_start: 0.6667 (mtt180) cc_final: 0.6448 (mtt-85) REVERT: G 1118 ASP cc_start: 0.6981 (t70) cc_final: 0.6666 (t70) REVERT: G 1125 ASN cc_start: 0.7644 (p0) cc_final: 0.7267 (p0) outliers start: 193 outliers final: 139 residues processed: 675 average time/residue: 0.4259 time to fit residues: 448.3408 Evaluate side-chains 663 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 509 time to evaluate : 3.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 851 CYS Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 921 LYS Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 973 ILE Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1073 LYS Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 190 HIS Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 188 ARG Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 317 ASN Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 615 VAL Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 935 GLN Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 0.8980 chunk 255 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 37 optimal weight: 40.0000 chunk 161 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 340 optimal weight: 1.9990 chunk 360 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 322 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 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 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A 965 GLN C 33 HIS D 121 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN ** D 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1106 GLN F 110 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 HIS ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 394 ASN ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 762 GLN ** G 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30124 Z= 0.302 Angle : 0.583 10.081 41029 Z= 0.299 Chirality : 0.045 0.285 4712 Planarity : 0.005 0.097 5285 Dihedral : 7.111 79.304 4746 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.54 % Favored : 90.38 % Rotamer: Outliers : 6.13 % Allowed : 15.78 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.13), residues: 3700 helix: -0.46 (0.21), residues: 651 sheet: -1.59 (0.17), residues: 862 loop : -2.88 (0.12), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 64 HIS 0.027 0.001 HIS F 190 PHE 0.026 0.002 PHE A 541 TYR 0.027 0.001 TYR D1067 ARG 0.006 0.000 ARG F 191 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 533 time to evaluate : 3.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.8479 (t) cc_final: 0.8216 (m) REVERT: A 90 VAL cc_start: 0.8047 (m) cc_final: 0.7831 (p) REVERT: A 101 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7075 (tp) REVERT: A 105 ILE cc_start: 0.8132 (mt) cc_final: 0.7835 (mm) REVERT: A 132 GLU cc_start: 0.7014 (mp0) cc_final: 0.6362 (mp0) REVERT: A 133 PHE cc_start: 0.8519 (m-80) cc_final: 0.7907 (m-80) REVERT: A 168 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: A 188 ARG cc_start: 0.7614 (ptp-170) cc_final: 0.7158 (mtt-85) REVERT: A 200 LYS cc_start: 0.7987 (mttm) cc_final: 0.7745 (mttt) REVERT: A 220 PHE cc_start: 0.8077 (t80) cc_final: 0.7830 (t80) REVERT: A 231 ILE cc_start: 0.8180 (mt) cc_final: 0.7948 (tt) REVERT: A 269 TYR cc_start: 0.7747 (m-80) cc_final: 0.7306 (m-80) REVERT: A 316 SER cc_start: 0.8119 (t) cc_final: 0.7864 (p) REVERT: A 324 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6349 (tm-30) REVERT: A 325 SER cc_start: 0.8159 (m) cc_final: 0.7146 (m) REVERT: A 517 LEU cc_start: 0.3291 (OUTLIER) cc_final: 0.2934 (tm) REVERT: A 532 ASN cc_start: 0.7741 (t0) cc_final: 0.7094 (t0) REVERT: A 605 SER cc_start: 0.7961 (p) cc_final: 0.7758 (t) REVERT: A 675 GLN cc_start: 0.6600 (mm-40) cc_final: 0.6318 (mm-40) REVERT: A 776 LYS cc_start: 0.7857 (ttpt) cc_final: 0.7517 (ttpt) REVERT: A 787 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7624 (mt0) REVERT: A 795 LYS cc_start: 0.7983 (mptm) cc_final: 0.7677 (mptt) REVERT: A 947 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7934 (mtpp) REVERT: A 949 GLN cc_start: 0.7872 (mm110) cc_final: 0.7573 (mm-40) REVERT: A 969 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7606 (pptt) REVERT: A 979 ASP cc_start: 0.6622 (t0) cc_final: 0.6190 (t0) REVERT: A 983 ARG cc_start: 0.7034 (mtp-110) cc_final: 0.6810 (mtp-110) REVERT: A 1002 GLN cc_start: 0.7024 (mt0) cc_final: 0.6763 (mt0) REVERT: A 1017 GLU cc_start: 0.7273 (tm-30) cc_final: 0.6907 (tm-30) REVERT: D 83 VAL cc_start: 0.7978 (OUTLIER) cc_final: 0.7593 (p) REVERT: D 105 ILE cc_start: 0.8037 (OUTLIER) cc_final: 0.7709 (mt) REVERT: D 169 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7459 (tm-30) REVERT: D 239 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6662 (tm-30) REVERT: D 294 ASP cc_start: 0.6943 (p0) cc_final: 0.6741 (p0) REVERT: D 319 ARG cc_start: 0.7382 (ttm170) cc_final: 0.7086 (ttm-80) REVERT: D 346 ARG cc_start: 0.7628 (mtt-85) cc_final: 0.7268 (mtt-85) REVERT: D 599 THR cc_start: 0.8169 (m) cc_final: 0.7890 (p) REVERT: D 705 VAL cc_start: 0.8640 (t) cc_final: 0.8405 (p) REVERT: D 790 LYS cc_start: 0.7867 (mtpp) cc_final: 0.7657 (mtpp) REVERT: D 804 GLN cc_start: 0.7887 (mt0) cc_final: 0.7616 (mt0) REVERT: D 808 ASP cc_start: 0.7208 (t0) cc_final: 0.6750 (p0) REVERT: D 960 ASN cc_start: 0.7922 (m110) cc_final: 0.7711 (m-40) REVERT: D 988 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6362 (tm-30) REVERT: D 992 GLN cc_start: 0.7213 (mt0) cc_final: 0.6970 (mt0) REVERT: D 1005 GLN cc_start: 0.7443 (tt0) cc_final: 0.7173 (tt0) REVERT: D 1029 MET cc_start: 0.7860 (ttm) cc_final: 0.7648 (ttm) REVERT: D 1072 GLU cc_start: 0.7722 (pm20) cc_final: 0.7394 (pm20) REVERT: D 1118 ASP cc_start: 0.6949 (t0) cc_final: 0.6318 (t0) REVERT: D 1141 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8079 (mp) REVERT: F 200 GLU cc_start: 0.0666 (OUTLIER) cc_final: 0.0149 (pm20) REVERT: G 47 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8364 (t) REVERT: G 54 LEU cc_start: 0.8254 (mt) cc_final: 0.8005 (mp) REVERT: G 63 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7389 (m) REVERT: G 117 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.6960 (mt) REVERT: G 186 ASN cc_start: 0.7380 (p0) cc_final: 0.6806 (p0) REVERT: G 190 PHE cc_start: 0.8006 (m-80) cc_final: 0.7791 (m-80) REVERT: G 203 SER cc_start: 0.8108 (OUTLIER) cc_final: 0.7868 (p) REVERT: G 286 THR cc_start: 0.7362 (p) cc_final: 0.7134 (t) REVERT: G 310 LYS cc_start: 0.8230 (ttpt) cc_final: 0.8009 (ttpt) REVERT: G 339 ASP cc_start: 0.7510 (p0) cc_final: 0.7267 (p0) REVERT: G 364 ASP cc_start: 0.7237 (t70) cc_final: 0.6830 (t70) REVERT: G 378 LYS cc_start: 0.7556 (tptm) cc_final: 0.7331 (tptm) REVERT: G 453 TYR cc_start: 0.5650 (t80) cc_final: 0.5343 (t80) REVERT: G 493 ARG cc_start: 0.6706 (OUTLIER) cc_final: 0.6358 (mmp-170) REVERT: G 546 LEU cc_start: 0.7825 (tm) cc_final: 0.7544 (tt) REVERT: G 574 ASP cc_start: 0.7004 (t0) cc_final: 0.6734 (t0) REVERT: G 578 ASP cc_start: 0.7148 (t0) cc_final: 0.6857 (t0) REVERT: G 599 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8352 (p) REVERT: G 764 LYS cc_start: 0.8131 (tttt) cc_final: 0.7799 (ttmm) REVERT: G 775 ASP cc_start: 0.7488 (m-30) cc_final: 0.7065 (m-30) REVERT: G 776 LYS cc_start: 0.7707 (ttpt) cc_final: 0.7506 (ttpt) REVERT: G 790 LYS cc_start: 0.7570 (mtmm) cc_final: 0.7368 (mtmm) REVERT: G 819 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7044 (mt-10) REVERT: G 821 LEU cc_start: 0.8084 (tt) cc_final: 0.7743 (tp) REVERT: G 855 PHE cc_start: 0.8068 (m-10) cc_final: 0.7737 (m-10) REVERT: G 921 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7499 (mmmt) REVERT: G 949 GLN cc_start: 0.8046 (mm-40) cc_final: 0.7656 (mm-40) REVERT: G 993 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7876 (mt) REVERT: G 998 THR cc_start: 0.8238 (t) cc_final: 0.8029 (p) REVERT: G 1017 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6652 (tm-30) REVERT: G 1072 GLU cc_start: 0.7863 (pm20) cc_final: 0.7502 (pm20) REVERT: G 1125 ASN cc_start: 0.7874 (p0) cc_final: 0.7065 (p0) REVERT: G 1127 ASP cc_start: 0.6598 (p0) cc_final: 0.6228 (p0) outliers start: 197 outliers final: 145 residues processed: 680 average time/residue: 0.4295 time to fit residues: 455.0602 Evaluate side-chains 681 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 518 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 198 TYR Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 779 GLN Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 851 CYS Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 323 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 605 SER Chi-restraints excluded: chain G residue 615 VAL Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 993 ILE Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1104 VAL Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 5.9990 chunk 204 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 307 optimal weight: 0.5980 chunk 249 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 323 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN D 121 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 GLN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 901 GLN D 913 GLN D 949 GLN F 110 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 641 ASN G 895 GLN ** G 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1002 GLN G1005 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30124 Z= 0.228 Angle : 0.551 10.247 41029 Z= 0.283 Chirality : 0.044 0.292 4712 Planarity : 0.005 0.101 5285 Dihedral : 6.936 79.547 4735 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.16 % Favored : 90.78 % Rotamer: Outliers : 5.94 % Allowed : 17.15 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.13), residues: 3700 helix: -0.07 (0.21), residues: 650 sheet: -1.31 (0.17), residues: 869 loop : -2.76 (0.12), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 64 HIS 0.004 0.001 HIS G1088 PHE 0.030 0.002 PHE A 855 TYR 0.023 0.001 TYR D1067 ARG 0.005 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 533 time to evaluate : 3.044 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 62 VAL cc_start: 0.8510 (t) cc_final: 0.8251 (m) REVERT: A 101 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7128 (tp) REVERT: A 102 ARG cc_start: 0.7253 (mtm-85) cc_final: 0.7037 (ptp90) REVERT: A 132 GLU cc_start: 0.6989 (mp0) cc_final: 0.6332 (mp0) REVERT: A 133 PHE cc_start: 0.8516 (m-80) cc_final: 0.7760 (m-80) REVERT: A 168 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: A 188 ARG cc_start: 0.7599 (ptp-170) cc_final: 0.7143 (mtt-85) REVERT: A 200 LYS cc_start: 0.7946 (mttm) cc_final: 0.7658 (mttp) REVERT: A 212 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6595 (mm-30) REVERT: A 220 PHE cc_start: 0.8135 (t80) cc_final: 0.7791 (t80) REVERT: A 231 ILE cc_start: 0.8198 (mt) cc_final: 0.7982 (tt) REVERT: A 237 ARG cc_start: 0.7626 (mmm-85) cc_final: 0.7248 (mtm-85) REVERT: A 269 TYR cc_start: 0.7780 (m-80) cc_final: 0.7252 (m-80) REVERT: A 316 SER cc_start: 0.7958 (t) cc_final: 0.7605 (p) REVERT: A 324 GLU cc_start: 0.6542 (tt0) cc_final: 0.6335 (tt0) REVERT: A 325 SER cc_start: 0.8195 (m) cc_final: 0.7867 (t) REVERT: A 517 LEU cc_start: 0.3292 (OUTLIER) cc_final: 0.2911 (tm) REVERT: A 532 ASN cc_start: 0.7808 (t0) cc_final: 0.7157 (t0) REVERT: A 605 SER cc_start: 0.8023 (p) cc_final: 0.7789 (t) REVERT: A 675 GLN cc_start: 0.6567 (mm-40) cc_final: 0.6309 (mm-40) REVERT: A 745 ASP cc_start: 0.6597 (p0) cc_final: 0.6141 (p0) REVERT: A 776 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7507 (ttpt) REVERT: A 787 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7665 (mt0) REVERT: A 795 LYS cc_start: 0.7997 (mptm) cc_final: 0.7712 (mptt) REVERT: A 804 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7242 (mm-40) REVERT: A 947 LYS cc_start: 0.8233 (mtpt) cc_final: 0.7953 (mtpp) REVERT: A 949 GLN cc_start: 0.7926 (mm-40) cc_final: 0.7593 (mm-40) REVERT: A 960 ASN cc_start: 0.7783 (t0) cc_final: 0.7529 (t0) REVERT: A 969 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7570 (pptt) REVERT: A 979 ASP cc_start: 0.6813 (t0) cc_final: 0.6320 (t0) REVERT: A 1017 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6836 (tm-30) REVERT: B 121 LEU cc_start: 0.2096 (OUTLIER) cc_final: 0.1851 (tt) REVERT: D 83 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7647 (p) REVERT: D 105 ILE cc_start: 0.7865 (mt) cc_final: 0.7479 (mt) REVERT: D 106 PHE cc_start: 0.7218 (m-80) cc_final: 0.6983 (m-80) REVERT: D 190 PHE cc_start: 0.7755 (m-80) cc_final: 0.7532 (m-80) REVERT: D 239 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: D 290 ASP cc_start: 0.7601 (t70) cc_final: 0.7243 (t0) REVERT: D 294 ASP cc_start: 0.6926 (p0) cc_final: 0.6623 (p0) REVERT: D 317 ASN cc_start: 0.7267 (m-40) cc_final: 0.7049 (m-40) REVERT: D 319 ARG cc_start: 0.7380 (ttm170) cc_final: 0.7089 (ttm-80) REVERT: D 346 ARG cc_start: 0.7681 (mtt-85) cc_final: 0.7326 (mtt-85) REVERT: D 599 THR cc_start: 0.8134 (m) cc_final: 0.7806 (p) REVERT: D 705 VAL cc_start: 0.8601 (t) cc_final: 0.8393 (p) REVERT: D 730 SER cc_start: 0.8536 (t) cc_final: 0.8323 (m) REVERT: D 737 ASP cc_start: 0.6886 (t0) cc_final: 0.6468 (t0) REVERT: D 790 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7648 (mtpp) REVERT: D 988 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: D 992 GLN cc_start: 0.7220 (mt0) cc_final: 0.6757 (mt0) REVERT: D 995 ARG cc_start: 0.8224 (mtm-85) cc_final: 0.8002 (mtm-85) REVERT: D 1005 GLN cc_start: 0.7398 (tt0) cc_final: 0.7150 (tt0) REVERT: D 1072 GLU cc_start: 0.7720 (pm20) cc_final: 0.7400 (pm20) REVERT: D 1118 ASP cc_start: 0.6744 (t0) cc_final: 0.6405 (t0) REVERT: D 1141 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8029 (mp) REVERT: F 200 GLU cc_start: 0.0877 (OUTLIER) cc_final: 0.0285 (pm20) REVERT: G 51 THR cc_start: 0.8650 (p) cc_final: 0.8394 (p) REVERT: G 63 THR cc_start: 0.7643 (OUTLIER) cc_final: 0.7416 (m) REVERT: G 117 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7049 (mt) REVERT: G 129 LYS cc_start: 0.7977 (mtmt) cc_final: 0.7498 (ptpt) REVERT: G 186 ASN cc_start: 0.7386 (p0) cc_final: 0.6783 (p0) REVERT: G 203 SER cc_start: 0.8046 (OUTLIER) cc_final: 0.7814 (p) REVERT: G 237 ARG cc_start: 0.7743 (mtp180) cc_final: 0.7539 (mtp-110) REVERT: G 286 THR cc_start: 0.7345 (p) cc_final: 0.7019 (t) REVERT: G 364 ASP cc_start: 0.7243 (t70) cc_final: 0.6858 (t70) REVERT: G 453 TYR cc_start: 0.5668 (t80) cc_final: 0.5402 (t80) REVERT: G 493 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.6338 (mmp-170) REVERT: G 546 LEU cc_start: 0.7871 (tm) cc_final: 0.7607 (tt) REVERT: G 599 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8332 (p) REVERT: G 641 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7570 (p0) REVERT: G 654 GLU cc_start: 0.7320 (pm20) cc_final: 0.7068 (pm20) REVERT: G 655 TYR cc_start: 0.7949 (t80) cc_final: 0.7566 (t80) REVERT: G 764 LYS cc_start: 0.8072 (tttt) cc_final: 0.7756 (ttmt) REVERT: G 790 LYS cc_start: 0.7536 (mtmm) cc_final: 0.7335 (mtmm) REVERT: G 819 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7067 (mt-10) REVERT: G 855 PHE cc_start: 0.8075 (m-10) cc_final: 0.7806 (m-10) REVERT: G 945 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8064 (mp) REVERT: G 949 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7673 (mm-40) REVERT: G 1017 GLU cc_start: 0.7047 (tm-30) cc_final: 0.6682 (tm-30) REVERT: G 1072 GLU cc_start: 0.7660 (pm20) cc_final: 0.7395 (pm20) outliers start: 191 outliers final: 137 residues processed: 679 average time/residue: 0.4284 time to fit residues: 454.5743 Evaluate side-chains 660 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 505 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 649 CYS Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1081 ILE Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 641 ASN Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 945 LEU Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 50.0000 chunk 324 optimal weight: 0.0870 chunk 71 optimal weight: 0.7980 chunk 211 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 360 optimal weight: 1.9990 chunk 299 optimal weight: 0.9990 chunk 167 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 119 optimal weight: 0.7980 chunk 189 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 540 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 949 GLN D 121 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 913 GLN ** D 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** F 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 HIS ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 GLN ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 641 ASN G1005 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30124 Z= 0.195 Angle : 0.547 11.330 41029 Z= 0.279 Chirality : 0.044 0.240 4712 Planarity : 0.005 0.103 5285 Dihedral : 6.710 79.631 4730 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.97 % Favored : 90.97 % Rotamer: Outliers : 6.10 % Allowed : 17.43 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.13), residues: 3700 helix: 0.19 (0.22), residues: 648 sheet: -1.21 (0.17), residues: 871 loop : -2.65 (0.12), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 64 HIS 0.004 0.001 HIS A1088 PHE 0.022 0.001 PHE A 541 TYR 0.020 0.001 TYR D1067 ARG 0.009 0.000 ARG G 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 522 time to evaluate : 3.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.8505 (t) cc_final: 0.8253 (m) REVERT: A 99 ASN cc_start: 0.7391 (p0) cc_final: 0.7103 (p0) REVERT: A 101 ILE cc_start: 0.7591 (OUTLIER) cc_final: 0.7071 (tp) REVERT: A 132 GLU cc_start: 0.6940 (mp0) cc_final: 0.6040 (mp0) REVERT: A 133 PHE cc_start: 0.8476 (m-80) cc_final: 0.7717 (m-80) REVERT: A 165 ASN cc_start: 0.7633 (OUTLIER) cc_final: 0.7122 (p0) REVERT: A 200 LYS cc_start: 0.7916 (mttm) cc_final: 0.7706 (mttm) REVERT: A 212 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6410 (mm-30) REVERT: A 220 PHE cc_start: 0.8081 (t80) cc_final: 0.7833 (t80) REVERT: A 231 ILE cc_start: 0.8209 (mt) cc_final: 0.7989 (tt) REVERT: A 237 ARG cc_start: 0.7635 (mmm-85) cc_final: 0.7258 (mtm-85) REVERT: A 269 TYR cc_start: 0.7788 (m-80) cc_final: 0.7227 (m-80) REVERT: A 316 SER cc_start: 0.7745 (t) cc_final: 0.7368 (p) REVERT: A 325 SER cc_start: 0.8124 (m) cc_final: 0.7785 (t) REVERT: A 517 LEU cc_start: 0.3276 (OUTLIER) cc_final: 0.2915 (tm) REVERT: A 532 ASN cc_start: 0.7759 (t0) cc_final: 0.7095 (t0) REVERT: A 558 LYS cc_start: 0.7348 (mmtm) cc_final: 0.7064 (mmmt) REVERT: A 605 SER cc_start: 0.8041 (p) cc_final: 0.7820 (t) REVERT: A 675 GLN cc_start: 0.6557 (mm-40) cc_final: 0.6296 (mm-40) REVERT: A 745 ASP cc_start: 0.6660 (p0) cc_final: 0.6217 (p0) REVERT: A 765 ARG cc_start: 0.7529 (ttm110) cc_final: 0.7128 (mtm-85) REVERT: A 776 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7479 (ttpt) REVERT: A 787 GLN cc_start: 0.8196 (mm-40) cc_final: 0.7681 (mt0) REVERT: A 795 LYS cc_start: 0.7996 (mptm) cc_final: 0.7708 (mptt) REVERT: A 804 GLN cc_start: 0.7780 (mm-40) cc_final: 0.7223 (mm-40) REVERT: A 947 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7985 (mtpp) REVERT: A 949 GLN cc_start: 0.7894 (mm110) cc_final: 0.7625 (mm-40) REVERT: A 960 ASN cc_start: 0.7780 (t0) cc_final: 0.7517 (t0) REVERT: A 969 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7576 (pptt) REVERT: A 979 ASP cc_start: 0.6820 (t0) cc_final: 0.6364 (t0) REVERT: A 1017 GLU cc_start: 0.7280 (tm-30) cc_final: 0.6742 (tm-30) REVERT: A 1094 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7783 (p) REVERT: B 121 LEU cc_start: 0.2188 (OUTLIER) cc_final: 0.1941 (tt) REVERT: D 29 THR cc_start: 0.8383 (m) cc_final: 0.8095 (m) REVERT: D 41 LYS cc_start: 0.8375 (mttt) cc_final: 0.8008 (mtmm) REVERT: D 83 VAL cc_start: 0.7992 (OUTLIER) cc_final: 0.7676 (p) REVERT: D 105 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7403 (mt) REVERT: D 106 PHE cc_start: 0.7283 (m-80) cc_final: 0.6995 (m-10) REVERT: D 190 PHE cc_start: 0.7731 (m-80) cc_final: 0.7509 (m-80) REVERT: D 239 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6705 (tm-30) REVERT: D 290 ASP cc_start: 0.7586 (t70) cc_final: 0.7255 (t0) REVERT: D 294 ASP cc_start: 0.6879 (p0) cc_final: 0.6409 (p0) REVERT: D 319 ARG cc_start: 0.7363 (ttm170) cc_final: 0.7084 (ttm-80) REVERT: D 346 ARG cc_start: 0.7679 (mtt-85) cc_final: 0.7334 (mtt-85) REVERT: D 599 THR cc_start: 0.8111 (m) cc_final: 0.7782 (p) REVERT: D 730 SER cc_start: 0.8522 (t) cc_final: 0.8296 (m) REVERT: D 790 LYS cc_start: 0.7843 (mtpp) cc_final: 0.7623 (mtpp) REVERT: D 808 ASP cc_start: 0.7181 (t0) cc_final: 0.6773 (p0) REVERT: D 851 CYS cc_start: 0.7936 (t) cc_final: 0.7636 (m) REVERT: D 854 LYS cc_start: 0.8490 (ttmm) cc_final: 0.8146 (ttpp) REVERT: D 904 TYR cc_start: 0.6904 (m-10) cc_final: 0.6315 (m-10) REVERT: D 988 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6192 (tm-30) REVERT: D 990 GLU cc_start: 0.7108 (mp0) cc_final: 0.6575 (mp0) REVERT: D 995 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7902 (mtp85) REVERT: D 1005 GLN cc_start: 0.7391 (tt0) cc_final: 0.7158 (tt0) REVERT: D 1072 GLU cc_start: 0.7716 (pm20) cc_final: 0.7421 (pm20) REVERT: D 1086 LYS cc_start: 0.8254 (ptmt) cc_final: 0.7970 (ptpp) REVERT: D 1118 ASP cc_start: 0.6790 (t0) cc_final: 0.6352 (t0) REVERT: D 1141 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8015 (mp) REVERT: F 200 GLU cc_start: 0.0861 (OUTLIER) cc_final: 0.0292 (pm20) REVERT: G 32 PHE cc_start: 0.7878 (m-80) cc_final: 0.7640 (m-10) REVERT: G 47 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8285 (t) REVERT: G 54 LEU cc_start: 0.8450 (mp) cc_final: 0.8145 (mt) REVERT: G 63 THR cc_start: 0.7607 (OUTLIER) cc_final: 0.6517 (t) REVERT: G 117 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7079 (mt) REVERT: G 129 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7530 (ptpt) REVERT: G 186 ASN cc_start: 0.7349 (p0) cc_final: 0.6747 (p0) REVERT: G 189 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6753 (mp0) REVERT: G 203 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7826 (p) REVERT: G 286 THR cc_start: 0.7295 (p) cc_final: 0.7067 (t) REVERT: G 364 ASP cc_start: 0.7257 (t70) cc_final: 0.6873 (t70) REVERT: G 453 TYR cc_start: 0.5750 (t80) cc_final: 0.5396 (t80) REVERT: G 493 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.6287 (mmp-170) REVERT: G 546 LEU cc_start: 0.7840 (tm) cc_final: 0.7551 (tt) REVERT: G 599 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8347 (p) REVERT: G 643 PHE cc_start: 0.8009 (t80) cc_final: 0.7737 (t80) REVERT: G 655 TYR cc_start: 0.7826 (t80) cc_final: 0.7534 (t80) REVERT: G 764 LYS cc_start: 0.8017 (tttt) cc_final: 0.7678 (ttmm) REVERT: G 790 LYS cc_start: 0.7421 (mtmm) cc_final: 0.7214 (mtmm) REVERT: G 819 GLU cc_start: 0.7507 (mt-10) cc_final: 0.6971 (mt-10) REVERT: G 855 PHE cc_start: 0.8066 (m-10) cc_final: 0.7807 (m-10) REVERT: G 949 GLN cc_start: 0.8036 (mm-40) cc_final: 0.7670 (mm-40) REVERT: G 1017 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6666 (tm-30) REVERT: G 1072 GLU cc_start: 0.7639 (pm20) cc_final: 0.7330 (pm20) REVERT: G 1107 ARG cc_start: 0.6730 (mtm-85) cc_final: 0.5939 (mtt-85) outliers start: 196 outliers final: 153 residues processed: 670 average time/residue: 0.4330 time to fit residues: 451.6267 Evaluate side-chains 674 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 501 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 239 GLN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 569 ILE Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 723 THR Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 128 GLN Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 314 GLN Chi-restraints excluded: chain G residue 323 THR Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 542 ASN Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 605 SER Chi-restraints excluded: chain G residue 641 ASN Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 935 GLN Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1136 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 1.9990 chunk 40 optimal weight: 50.0000 chunk 205 optimal weight: 0.8980 chunk 263 optimal weight: 7.9990 chunk 204 optimal weight: 0.9990 chunk 303 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 359 optimal weight: 0.9990 chunk 224 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 chunk 165 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 762 GLN A 949 GLN D 87 ASN D 121 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 913 GLN D 935 GLN D1002 GLN F 110 GLN F 128 GLN G 66 HIS G 122 ASN ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 564 GLN G 641 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30124 Z= 0.254 Angle : 0.566 9.890 41029 Z= 0.289 Chirality : 0.044 0.255 4712 Planarity : 0.005 0.099 5285 Dihedral : 6.709 79.641 4728 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.49 % Favored : 90.46 % Rotamer: Outliers : 6.29 % Allowed : 17.68 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.13), residues: 3700 helix: 0.29 (0.22), residues: 648 sheet: -1.13 (0.17), residues: 863 loop : -2.58 (0.12), residues: 2189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 64 HIS 0.004 0.001 HIS G1088 PHE 0.026 0.002 PHE G 329 TYR 0.024 0.001 TYR D1067 ARG 0.007 0.000 ARG D1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 516 time to evaluate : 3.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.8517 (t) cc_final: 0.8253 (m) REVERT: A 82 PRO cc_start: 0.8662 (Cg_endo) cc_final: 0.8411 (Cg_exo) REVERT: A 99 ASN cc_start: 0.7405 (p0) cc_final: 0.7204 (p0) REVERT: A 101 ILE cc_start: 0.7665 (OUTLIER) cc_final: 0.7135 (tp) REVERT: A 132 GLU cc_start: 0.6918 (mp0) cc_final: 0.6107 (mp0) REVERT: A 133 PHE cc_start: 0.8469 (m-80) cc_final: 0.7706 (m-80) REVERT: A 165 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7204 (p0) REVERT: A 200 LYS cc_start: 0.7966 (mttm) cc_final: 0.7715 (mttt) REVERT: A 212 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6338 (mm-30) REVERT: A 220 PHE cc_start: 0.8163 (t80) cc_final: 0.7920 (t80) REVERT: A 237 ARG cc_start: 0.7631 (mmm-85) cc_final: 0.7260 (mtm-85) REVERT: A 269 TYR cc_start: 0.7802 (m-80) cc_final: 0.7353 (m-80) REVERT: A 316 SER cc_start: 0.7754 (t) cc_final: 0.7505 (p) REVERT: A 325 SER cc_start: 0.8125 (m) cc_final: 0.7915 (t) REVERT: A 517 LEU cc_start: 0.3266 (OUTLIER) cc_final: 0.2902 (tm) REVERT: A 532 ASN cc_start: 0.7846 (t0) cc_final: 0.7176 (t0) REVERT: A 675 GLN cc_start: 0.6584 (mm-40) cc_final: 0.6320 (mm-40) REVERT: A 702 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6244 (tp30) REVERT: A 745 ASP cc_start: 0.6807 (p0) cc_final: 0.6283 (p0) REVERT: A 765 ARG cc_start: 0.7551 (ttm110) cc_final: 0.7148 (mtm-85) REVERT: A 776 LYS cc_start: 0.7836 (ttpt) cc_final: 0.7484 (ttpt) REVERT: A 787 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7693 (mt0) REVERT: A 795 LYS cc_start: 0.8026 (mptm) cc_final: 0.7755 (mptm) REVERT: A 947 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7992 (mtpp) REVERT: A 949 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7644 (mm-40) REVERT: A 960 ASN cc_start: 0.7787 (t0) cc_final: 0.7513 (t0) REVERT: A 969 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7539 (pptt) REVERT: A 979 ASP cc_start: 0.6870 (t0) cc_final: 0.6357 (t0) REVERT: A 1017 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6859 (tm-30) REVERT: B 121 LEU cc_start: 0.2177 (OUTLIER) cc_final: 0.1929 (tt) REVERT: D 29 THR cc_start: 0.8364 (m) cc_final: 0.8074 (m) REVERT: D 41 LYS cc_start: 0.8391 (mttt) cc_final: 0.8032 (mtmm) REVERT: D 83 VAL cc_start: 0.7993 (OUTLIER) cc_final: 0.7697 (p) REVERT: D 105 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7615 (mt) REVERT: D 117 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7761 (tm) REVERT: D 169 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7465 (tm-30) REVERT: D 190 PHE cc_start: 0.7770 (m-80) cc_final: 0.7556 (m-80) REVERT: D 239 GLN cc_start: 0.7055 (tm-30) cc_final: 0.6705 (tm-30) REVERT: D 290 ASP cc_start: 0.7624 (t70) cc_final: 0.7251 (t0) REVERT: D 294 ASP cc_start: 0.6925 (p0) cc_final: 0.6402 (p0) REVERT: D 319 ARG cc_start: 0.7356 (ttm170) cc_final: 0.7109 (ttm-80) REVERT: D 346 ARG cc_start: 0.7686 (mtt-85) cc_final: 0.7313 (mtt-85) REVERT: D 599 THR cc_start: 0.8121 (m) cc_final: 0.7762 (p) REVERT: D 730 SER cc_start: 0.8490 (t) cc_final: 0.8260 (m) REVERT: D 776 LYS cc_start: 0.7872 (ttpp) cc_final: 0.7613 (ttmm) REVERT: D 790 LYS cc_start: 0.7839 (mtpp) cc_final: 0.7618 (mtpp) REVERT: D 804 GLN cc_start: 0.8104 (mt0) cc_final: 0.7901 (mm-40) REVERT: D 808 ASP cc_start: 0.7233 (t0) cc_final: 0.6787 (p0) REVERT: D 854 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8115 (ttpp) REVERT: D 947 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8201 (mtpt) REVERT: D 988 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6093 (tm-30) REVERT: D 995 ARG cc_start: 0.8211 (mtm-85) cc_final: 0.7918 (mtp85) REVERT: D 1005 GLN cc_start: 0.7421 (tt0) cc_final: 0.7189 (tt0) REVERT: D 1086 LYS cc_start: 0.8243 (ptmt) cc_final: 0.7957 (ptpp) REVERT: D 1118 ASP cc_start: 0.6810 (t0) cc_final: 0.6387 (t0) REVERT: D 1141 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8019 (mp) REVERT: F 200 GLU cc_start: 0.0806 (OUTLIER) cc_final: 0.0257 (pm20) REVERT: G 47 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8289 (t) REVERT: G 63 THR cc_start: 0.7597 (OUTLIER) cc_final: 0.6553 (t) REVERT: G 104 TRP cc_start: 0.7919 (m-90) cc_final: 0.7418 (m-90) REVERT: G 117 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7219 (mt) REVERT: G 129 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7563 (ptpt) REVERT: G 186 ASN cc_start: 0.7382 (p0) cc_final: 0.6728 (p0) REVERT: G 189 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: G 203 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7818 (p) REVERT: G 286 THR cc_start: 0.7313 (p) cc_final: 0.7090 (t) REVERT: G 317 ASN cc_start: 0.7979 (m110) cc_final: 0.7635 (m-40) REVERT: G 364 ASP cc_start: 0.7265 (t70) cc_final: 0.6869 (t70) REVERT: G 453 TYR cc_start: 0.5758 (t80) cc_final: 0.5438 (t80) REVERT: G 493 ARG cc_start: 0.6714 (OUTLIER) cc_final: 0.6282 (mmp-170) REVERT: G 546 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7483 (tt) REVERT: G 599 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8368 (p) REVERT: G 764 LYS cc_start: 0.8055 (tttt) cc_final: 0.7709 (ttpp) REVERT: G 819 GLU cc_start: 0.7511 (mt-10) cc_final: 0.6981 (mt-10) REVERT: G 855 PHE cc_start: 0.8049 (m-10) cc_final: 0.7794 (m-80) REVERT: G 900 MET cc_start: 0.7662 (mmm) cc_final: 0.7444 (mmm) REVERT: G 949 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7664 (mm-40) REVERT: G 976 VAL cc_start: 0.8346 (t) cc_final: 0.8036 (m) REVERT: G 1017 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6657 (tm-30) REVERT: G 1072 GLU cc_start: 0.7662 (pm20) cc_final: 0.7363 (pm20) REVERT: G 1107 ARG cc_start: 0.6846 (mtm-85) cc_final: 0.6615 (mtt90) outliers start: 202 outliers final: 156 residues processed: 666 average time/residue: 0.4490 time to fit residues: 465.5277 Evaluate side-chains 680 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 502 time to evaluate : 3.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 132 GLU Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 528 LYS Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 704 SER Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 816 SER Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 203 SER Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 486 PHE Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 539 VAL Chi-restraints excluded: chain G residue 542 ASN Chi-restraints excluded: chain G residue 546 LEU Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 564 GLN Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 605 SER Chi-restraints excluded: chain G residue 641 ASN Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 663 ASP Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 762 GLN Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 935 GLN Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1136 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 214 optimal weight: 0.7980 chunk 108 optimal weight: 20.0000 chunk 70 optimal weight: 0.6980 chunk 69 optimal weight: 0.0060 chunk 228 optimal weight: 9.9990 chunk 244 optimal weight: 0.1980 chunk 177 optimal weight: 0.6980 chunk 33 optimal weight: 50.0000 chunk 282 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 913 GLN D 935 GLN F 110 GLN G 66 HIS ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 641 ASN G1106 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30124 Z= 0.177 Angle : 0.548 9.345 41029 Z= 0.279 Chirality : 0.044 0.234 4712 Planarity : 0.005 0.099 5285 Dihedral : 6.600 79.629 4722 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.14 % Favored : 90.81 % Rotamer: Outliers : 5.94 % Allowed : 18.46 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.14), residues: 3700 helix: 0.61 (0.22), residues: 643 sheet: -1.05 (0.17), residues: 864 loop : -2.49 (0.13), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 64 HIS 0.003 0.000 HIS G1088 PHE 0.037 0.001 PHE D 106 TYR 0.019 0.001 TYR D1067 ARG 0.007 0.000 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 510 time to evaluate : 3.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 VAL cc_start: 0.8516 (t) cc_final: 0.8270 (m) REVERT: A 82 PRO cc_start: 0.8670 (Cg_endo) cc_final: 0.8444 (Cg_exo) REVERT: A 101 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7090 (tp) REVERT: A 132 GLU cc_start: 0.7018 (mp0) cc_final: 0.6143 (mp0) REVERT: A 133 PHE cc_start: 0.8472 (m-80) cc_final: 0.7692 (m-80) REVERT: A 165 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7195 (p0) REVERT: A 168 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7773 (m-80) REVERT: A 200 LYS cc_start: 0.7919 (mttm) cc_final: 0.7655 (mttp) REVERT: A 212 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6217 (mm-30) REVERT: A 220 PHE cc_start: 0.8126 (t80) cc_final: 0.7839 (t80) REVERT: A 237 ARG cc_start: 0.7619 (mmm-85) cc_final: 0.7256 (mtm-85) REVERT: A 269 TYR cc_start: 0.7824 (m-80) cc_final: 0.7385 (m-80) REVERT: A 316 SER cc_start: 0.7770 (t) cc_final: 0.7483 (p) REVERT: A 325 SER cc_start: 0.8103 (m) cc_final: 0.7893 (t) REVERT: A 517 LEU cc_start: 0.3304 (OUTLIER) cc_final: 0.2937 (tm) REVERT: A 532 ASN cc_start: 0.7804 (t0) cc_final: 0.7154 (t0) REVERT: A 558 LYS cc_start: 0.7334 (mmtm) cc_final: 0.7068 (mmmt) REVERT: A 675 GLN cc_start: 0.6553 (mm-40) cc_final: 0.6290 (mm-40) REVERT: A 745 ASP cc_start: 0.6806 (p0) cc_final: 0.6255 (p0) REVERT: A 776 LYS cc_start: 0.7816 (ttpt) cc_final: 0.7459 (ttpt) REVERT: A 787 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7699 (mt0) REVERT: A 795 LYS cc_start: 0.8007 (mptm) cc_final: 0.7705 (mptt) REVERT: A 947 LYS cc_start: 0.8234 (mtpt) cc_final: 0.7958 (mtpp) REVERT: A 949 GLN cc_start: 0.7940 (mm-40) cc_final: 0.7638 (mm-40) REVERT: A 960 ASN cc_start: 0.7763 (t0) cc_final: 0.7478 (t0) REVERT: A 969 LYS cc_start: 0.8270 (OUTLIER) cc_final: 0.7493 (pptt) REVERT: A 979 ASP cc_start: 0.6845 (t0) cc_final: 0.6343 (t0) REVERT: A 1017 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6763 (tm-30) REVERT: A 1038 LYS cc_start: 0.8164 (mtmt) cc_final: 0.7873 (mtmt) REVERT: A 1073 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7721 (mtpp) REVERT: B 121 LEU cc_start: 0.2081 (OUTLIER) cc_final: 0.1836 (tt) REVERT: D 29 THR cc_start: 0.8305 (m) cc_final: 0.8000 (m) REVERT: D 41 LYS cc_start: 0.8368 (mttt) cc_final: 0.7993 (mtmm) REVERT: D 83 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7712 (p) REVERT: D 104 TRP cc_start: 0.6451 (m-90) cc_final: 0.6023 (m-90) REVERT: D 105 ILE cc_start: 0.7895 (OUTLIER) cc_final: 0.7496 (mt) REVERT: D 239 GLN cc_start: 0.7104 (tm-30) cc_final: 0.6743 (tm-30) REVERT: D 290 ASP cc_start: 0.7598 (t70) cc_final: 0.7251 (t0) REVERT: D 319 ARG cc_start: 0.7338 (ttm170) cc_final: 0.7086 (ttm-80) REVERT: D 346 ARG cc_start: 0.7686 (mtt-85) cc_final: 0.7324 (mtt-85) REVERT: D 524 VAL cc_start: 0.5715 (OUTLIER) cc_final: 0.5512 (p) REVERT: D 599 THR cc_start: 0.8091 (m) cc_final: 0.7761 (p) REVERT: D 730 SER cc_start: 0.8484 (t) cc_final: 0.8275 (m) REVERT: D 776 LYS cc_start: 0.7883 (ttpp) cc_final: 0.7610 (ttmm) REVERT: D 790 LYS cc_start: 0.7840 (mtpp) cc_final: 0.7618 (mtpp) REVERT: D 808 ASP cc_start: 0.7269 (t0) cc_final: 0.6791 (p0) REVERT: D 854 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8108 (ttpp) REVERT: D 947 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8133 (mtpt) REVERT: D 988 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6019 (tm-30) REVERT: D 995 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.7976 (mtm-85) REVERT: D 1005 GLN cc_start: 0.7383 (tt0) cc_final: 0.7161 (tt0) REVERT: D 1086 LYS cc_start: 0.8281 (ptmt) cc_final: 0.7855 (mtmm) REVERT: D 1118 ASP cc_start: 0.6730 (t0) cc_final: 0.6328 (t0) REVERT: D 1141 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8005 (mp) REVERT: F 200 GLU cc_start: 0.0800 (OUTLIER) cc_final: 0.0266 (pm20) REVERT: G 47 VAL cc_start: 0.8549 (OUTLIER) cc_final: 0.8286 (t) REVERT: G 63 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.6521 (t) REVERT: G 104 TRP cc_start: 0.7906 (m-90) cc_final: 0.7411 (m-90) REVERT: G 117 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7336 (mt) REVERT: G 129 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7522 (ptpt) REVERT: G 186 ASN cc_start: 0.7354 (p0) cc_final: 0.6716 (p0) REVERT: G 189 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: G 286 THR cc_start: 0.7300 (p) cc_final: 0.7074 (t) REVERT: G 339 ASP cc_start: 0.7771 (p0) cc_final: 0.7471 (p0) REVERT: G 364 ASP cc_start: 0.7241 (t70) cc_final: 0.6847 (t70) REVERT: G 453 TYR cc_start: 0.5734 (t80) cc_final: 0.5414 (t80) REVERT: G 493 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.6255 (mmp-170) REVERT: G 546 LEU cc_start: 0.7701 (tm) cc_final: 0.7400 (tt) REVERT: G 591 SER cc_start: 0.8404 (t) cc_final: 0.8178 (m) REVERT: G 599 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8355 (p) REVERT: G 654 GLU cc_start: 0.7429 (pm20) cc_final: 0.7198 (pm20) REVERT: G 764 LYS cc_start: 0.7992 (tttt) cc_final: 0.7652 (ttpp) REVERT: G 819 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7043 (mt-10) REVERT: G 855 PHE cc_start: 0.8014 (m-10) cc_final: 0.7811 (m-10) REVERT: G 900 MET cc_start: 0.7641 (mmm) cc_final: 0.7435 (mmm) REVERT: G 949 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7662 (mm-40) REVERT: G 976 VAL cc_start: 0.8358 (t) cc_final: 0.8041 (m) REVERT: G 1017 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6662 (tm-30) REVERT: G 1072 GLU cc_start: 0.7622 (pm20) cc_final: 0.7337 (pm20) REVERT: G 1107 ARG cc_start: 0.6759 (mtm-85) cc_final: 0.6450 (mtt-85) REVERT: G 1127 ASP cc_start: 0.7013 (m-30) cc_final: 0.6779 (m-30) outliers start: 191 outliers final: 146 residues processed: 655 average time/residue: 0.4389 time to fit residues: 448.2539 Evaluate side-chains 663 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 497 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 524 VAL Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 803 SER Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 914 ASN Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 988 GLU Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 323 THR Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 486 PHE Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 564 GLN Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 599 THR Chi-restraints excluded: chain G residue 605 SER Chi-restraints excluded: chain G residue 641 ASN Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 746 SER Chi-restraints excluded: chain G residue 762 GLN Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 935 GLN Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1136 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 2.9990 chunk 344 optimal weight: 0.1980 chunk 314 optimal weight: 4.9990 chunk 335 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 302 optimal weight: 0.7980 chunk 316 optimal weight: 0.6980 chunk 333 optimal weight: 0.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 872 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 919 ASN F 110 GLN G 66 HIS ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 641 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 30124 Z= 0.207 Angle : 0.565 10.616 41029 Z= 0.288 Chirality : 0.044 0.278 4712 Planarity : 0.005 0.098 5285 Dihedral : 6.527 79.534 4713 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.38 % Favored : 90.57 % Rotamer: Outliers : 5.79 % Allowed : 18.58 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.14), residues: 3700 helix: 0.65 (0.22), residues: 648 sheet: -1.04 (0.17), residues: 866 loop : -2.43 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 64 HIS 0.004 0.001 HIS G1088 PHE 0.023 0.001 PHE G 329 TYR 0.022 0.001 TYR D1067 ARG 0.006 0.000 ARG D1019 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 507 time to evaluate : 3.458 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 62 VAL cc_start: 0.8519 (t) cc_final: 0.8270 (m) REVERT: A 99 ASN cc_start: 0.7360 (p0) cc_final: 0.5923 (p0) REVERT: A 101 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7113 (tp) REVERT: A 132 GLU cc_start: 0.7015 (mp0) cc_final: 0.6111 (mp0) REVERT: A 133 PHE cc_start: 0.8461 (m-80) cc_final: 0.7690 (m-80) REVERT: A 165 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7180 (p0) REVERT: A 168 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.7805 (m-80) REVERT: A 200 LYS cc_start: 0.7928 (mttm) cc_final: 0.7675 (mttt) REVERT: A 212 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6252 (mm-30) REVERT: A 237 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.7267 (mtm-85) REVERT: A 269 TYR cc_start: 0.7885 (m-80) cc_final: 0.7493 (m-80) REVERT: A 316 SER cc_start: 0.7880 (t) cc_final: 0.7562 (p) REVERT: A 325 SER cc_start: 0.8112 (m) cc_final: 0.7882 (t) REVERT: A 517 LEU cc_start: 0.3299 (OUTLIER) cc_final: 0.2954 (tm) REVERT: A 532 ASN cc_start: 0.7858 (t0) cc_final: 0.7560 (t0) REVERT: A 558 LYS cc_start: 0.7341 (mmtm) cc_final: 0.7072 (mmmt) REVERT: A 675 GLN cc_start: 0.6569 (mm-40) cc_final: 0.6301 (mm-40) REVERT: A 745 ASP cc_start: 0.6876 (p0) cc_final: 0.6303 (p0) REVERT: A 773 GLU cc_start: 0.6548 (tt0) cc_final: 0.6327 (tt0) REVERT: A 776 LYS cc_start: 0.7818 (ttpt) cc_final: 0.7427 (ttpt) REVERT: A 787 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7813 (mt0) REVERT: A 795 LYS cc_start: 0.8022 (mptm) cc_final: 0.7723 (mptt) REVERT: A 947 LYS cc_start: 0.8245 (mtpt) cc_final: 0.7962 (mtpp) REVERT: A 949 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7647 (mm-40) REVERT: A 960 ASN cc_start: 0.7771 (t0) cc_final: 0.7493 (t0) REVERT: A 969 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7469 (pptt) REVERT: A 979 ASP cc_start: 0.6850 (t0) cc_final: 0.6300 (t0) REVERT: A 1017 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6867 (tm-30) REVERT: A 1038 LYS cc_start: 0.8170 (mtmt) cc_final: 0.7884 (mtmt) REVERT: A 1073 LYS cc_start: 0.8168 (mtmt) cc_final: 0.7660 (mtmm) REVERT: B 121 LEU cc_start: 0.2057 (OUTLIER) cc_final: 0.1821 (tt) REVERT: D 29 THR cc_start: 0.8267 (m) cc_final: 0.7982 (m) REVERT: D 41 LYS cc_start: 0.8375 (mttt) cc_final: 0.8005 (mtmm) REVERT: D 83 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7725 (p) REVERT: D 105 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7502 (mt) REVERT: D 239 GLN cc_start: 0.7135 (tm-30) cc_final: 0.6752 (tm-30) REVERT: D 290 ASP cc_start: 0.7616 (t70) cc_final: 0.7348 (t0) REVERT: D 294 ASP cc_start: 0.6905 (p0) cc_final: 0.6361 (p0) REVERT: D 319 ARG cc_start: 0.7343 (ttm170) cc_final: 0.7082 (ttm-80) REVERT: D 346 ARG cc_start: 0.7659 (mtt-85) cc_final: 0.7292 (mtt-85) REVERT: D 599 THR cc_start: 0.8088 (m) cc_final: 0.7766 (p) REVERT: D 730 SER cc_start: 0.8527 (t) cc_final: 0.8308 (m) REVERT: D 776 LYS cc_start: 0.7943 (ttpp) cc_final: 0.7675 (ttmm) REVERT: D 790 LYS cc_start: 0.7843 (mtpp) cc_final: 0.7620 (mtpp) REVERT: D 854 LYS cc_start: 0.8429 (ttmm) cc_final: 0.8083 (ttpp) REVERT: D 947 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8146 (mtpt) REVERT: D 995 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7994 (mtm-85) REVERT: D 1005 GLN cc_start: 0.7395 (tt0) cc_final: 0.7175 (tt0) REVERT: D 1086 LYS cc_start: 0.8243 (ptmt) cc_final: 0.7946 (pttt) REVERT: D 1118 ASP cc_start: 0.6772 (t0) cc_final: 0.6332 (t0) REVERT: D 1141 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8014 (mp) REVERT: F 200 GLU cc_start: 0.0747 (OUTLIER) cc_final: 0.0233 (pm20) REVERT: G 28 TYR cc_start: 0.7933 (m-80) cc_final: 0.7620 (m-80) REVERT: G 47 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8295 (t) REVERT: G 63 THR cc_start: 0.7612 (OUTLIER) cc_final: 0.6544 (t) REVERT: G 104 TRP cc_start: 0.7908 (m-90) cc_final: 0.7472 (m-90) REVERT: G 117 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7291 (mt) REVERT: G 129 LYS cc_start: 0.7974 (mtmt) cc_final: 0.7571 (ptpt) REVERT: G 186 ASN cc_start: 0.7398 (p0) cc_final: 0.6738 (p0) REVERT: G 286 THR cc_start: 0.7331 (p) cc_final: 0.7105 (t) REVERT: G 317 ASN cc_start: 0.7970 (m110) cc_final: 0.7662 (m-40) REVERT: G 364 ASP cc_start: 0.7265 (t70) cc_final: 0.6909 (t70) REVERT: G 453 TYR cc_start: 0.5720 (t80) cc_final: 0.5401 (t80) REVERT: G 478 LYS cc_start: 0.3592 (OUTLIER) cc_final: 0.3223 (tmmt) REVERT: G 493 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.6259 (mmp-170) REVERT: G 546 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7440 (tt) REVERT: G 591 SER cc_start: 0.8454 (t) cc_final: 0.8233 (m) REVERT: G 641 ASN cc_start: 0.7329 (OUTLIER) cc_final: 0.6946 (p0) REVERT: G 655 TYR cc_start: 0.7845 (t80) cc_final: 0.7376 (t80) REVERT: G 764 LYS cc_start: 0.8031 (tttt) cc_final: 0.7782 (ttmm) REVERT: G 819 GLU cc_start: 0.7504 (mt-10) cc_final: 0.6969 (mt-10) REVERT: G 855 PHE cc_start: 0.7990 (m-10) cc_final: 0.7776 (m-80) REVERT: G 900 MET cc_start: 0.7648 (mmm) cc_final: 0.7415 (mmm) REVERT: G 949 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7666 (mm-40) REVERT: G 976 VAL cc_start: 0.8297 (t) cc_final: 0.7994 (m) REVERT: G 1017 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6656 (tm-30) REVERT: G 1072 GLU cc_start: 0.7654 (pm20) cc_final: 0.7361 (pm20) REVERT: G 1107 ARG cc_start: 0.6735 (mtm-85) cc_final: 0.6532 (mtt90) REVERT: G 1127 ASP cc_start: 0.6992 (m-30) cc_final: 0.6780 (m-30) outliers start: 186 outliers final: 152 residues processed: 648 average time/residue: 0.4385 time to fit residues: 441.7104 Evaluate side-chains 668 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 497 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 878 LEU Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1050 MET Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 323 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 486 PHE Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 542 ASN Chi-restraints excluded: chain G residue 546 LEU Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 605 SER Chi-restraints excluded: chain G residue 641 ASN Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 746 SER Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 790 LYS Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 935 GLN Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1136 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 0.2980 chunk 354 optimal weight: 2.9990 chunk 216 optimal weight: 0.4980 chunk 168 optimal weight: 8.9990 chunk 246 optimal weight: 50.0000 chunk 371 optimal weight: 0.9990 chunk 342 optimal weight: 0.7980 chunk 295 optimal weight: 0.8980 chunk 30 optimal weight: 50.0000 chunk 228 optimal weight: 4.9990 chunk 181 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 314 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 644 GLN ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 913 GLN D1135 ASN F 110 GLN G 66 HIS ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN G 613 GLN G 641 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30124 Z= 0.210 Angle : 0.571 10.650 41029 Z= 0.290 Chirality : 0.044 0.252 4712 Planarity : 0.005 0.102 5285 Dihedral : 6.419 79.495 4707 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.49 % Favored : 90.46 % Rotamer: Outliers : 5.60 % Allowed : 19.05 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.14), residues: 3700 helix: 0.71 (0.22), residues: 649 sheet: -1.02 (0.17), residues: 867 loop : -2.38 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP A 64 HIS 0.005 0.001 HIS G1101 PHE 0.031 0.001 PHE D 106 TYR 0.025 0.001 TYR D 170 ARG 0.005 0.000 ARG D1019 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7400 Ramachandran restraints generated. 3700 Oldfield, 0 Emsley, 3700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 499 time to evaluate : 3.069 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 62 VAL cc_start: 0.8512 (t) cc_final: 0.8271 (m) REVERT: A 99 ASN cc_start: 0.6681 (p0) cc_final: 0.6460 (p0) REVERT: A 101 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7386 (tp) REVERT: A 102 ARG cc_start: 0.7064 (ptp90) cc_final: 0.6632 (ptp90) REVERT: A 132 GLU cc_start: 0.7009 (mp0) cc_final: 0.6113 (mp0) REVERT: A 133 PHE cc_start: 0.8461 (m-80) cc_final: 0.7686 (m-80) REVERT: A 165 ASN cc_start: 0.7691 (OUTLIER) cc_final: 0.7191 (p0) REVERT: A 168 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: A 200 LYS cc_start: 0.7898 (mttm) cc_final: 0.7654 (mttt) REVERT: A 212 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6265 (mm-30) REVERT: A 231 ILE cc_start: 0.8376 (tt) cc_final: 0.8038 (pt) REVERT: A 237 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7250 (mtm-85) REVERT: A 269 TYR cc_start: 0.7923 (m-80) cc_final: 0.7473 (m-80) REVERT: A 316 SER cc_start: 0.7860 (t) cc_final: 0.7572 (p) REVERT: A 325 SER cc_start: 0.8117 (m) cc_final: 0.7878 (t) REVERT: A 517 LEU cc_start: 0.3305 (OUTLIER) cc_final: 0.2957 (tm) REVERT: A 532 ASN cc_start: 0.7883 (t0) cc_final: 0.7591 (t0) REVERT: A 558 LYS cc_start: 0.7346 (mmtm) cc_final: 0.7069 (mmmt) REVERT: A 675 GLN cc_start: 0.6573 (mm-40) cc_final: 0.6271 (mm-40) REVERT: A 745 ASP cc_start: 0.6947 (p0) cc_final: 0.6379 (p0) REVERT: A 765 ARG cc_start: 0.7507 (ttm110) cc_final: 0.7137 (mtm-85) REVERT: A 773 GLU cc_start: 0.6555 (tt0) cc_final: 0.6332 (tt0) REVERT: A 776 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7430 (ttpt) REVERT: A 787 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7810 (mt0) REVERT: A 795 LYS cc_start: 0.8025 (mptm) cc_final: 0.7728 (mptt) REVERT: A 947 LYS cc_start: 0.8247 (mtpt) cc_final: 0.7967 (mtpp) REVERT: A 949 GLN cc_start: 0.7956 (mm-40) cc_final: 0.7651 (mm-40) REVERT: A 960 ASN cc_start: 0.7780 (t0) cc_final: 0.7484 (t0) REVERT: A 969 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7488 (pptt) REVERT: A 979 ASP cc_start: 0.6816 (t0) cc_final: 0.6288 (t0) REVERT: A 1017 GLU cc_start: 0.7279 (tm-30) cc_final: 0.6891 (tm-30) REVERT: A 1038 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7890 (mtmt) REVERT: A 1073 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7736 (mtpp) REVERT: B 121 LEU cc_start: 0.2065 (OUTLIER) cc_final: 0.1827 (tt) REVERT: D 29 THR cc_start: 0.8272 (m) cc_final: 0.8015 (m) REVERT: D 41 LYS cc_start: 0.8380 (mttt) cc_final: 0.7994 (mtmm) REVERT: D 83 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7734 (p) REVERT: D 105 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7609 (mt) REVERT: D 106 PHE cc_start: 0.7378 (m-80) cc_final: 0.7157 (m-80) REVERT: D 239 GLN cc_start: 0.7144 (tm-30) cc_final: 0.6756 (tm-30) REVERT: D 290 ASP cc_start: 0.7614 (t70) cc_final: 0.7352 (t0) REVERT: D 294 ASP cc_start: 0.6901 (p0) cc_final: 0.6357 (p0) REVERT: D 319 ARG cc_start: 0.7337 (ttm170) cc_final: 0.7075 (ttm-80) REVERT: D 346 ARG cc_start: 0.7703 (mtt-85) cc_final: 0.7328 (mtt-85) REVERT: D 599 THR cc_start: 0.8080 (m) cc_final: 0.7759 (p) REVERT: D 776 LYS cc_start: 0.7984 (ttpp) cc_final: 0.7716 (ttmm) REVERT: D 790 LYS cc_start: 0.7844 (mtpp) cc_final: 0.7619 (mtpp) REVERT: D 854 LYS cc_start: 0.8413 (ttmm) cc_final: 0.8091 (ttpp) REVERT: D 947 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.8131 (mtpt) REVERT: D 995 ARG cc_start: 0.8202 (mtm-85) cc_final: 0.7991 (mtm-85) REVERT: D 1005 GLN cc_start: 0.7400 (tt0) cc_final: 0.7176 (tt0) REVERT: D 1086 LYS cc_start: 0.8258 (ptmt) cc_final: 0.7945 (pttt) REVERT: D 1118 ASP cc_start: 0.6755 (t0) cc_final: 0.6353 (t0) REVERT: D 1141 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7996 (mp) REVERT: F 200 GLU cc_start: 0.0741 (OUTLIER) cc_final: 0.0239 (pm20) REVERT: G 47 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8290 (t) REVERT: G 63 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.6531 (t) REVERT: G 104 TRP cc_start: 0.7884 (m-90) cc_final: 0.7504 (m-90) REVERT: G 117 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7304 (mt) REVERT: G 129 LYS cc_start: 0.7988 (mtmt) cc_final: 0.7573 (ptpt) REVERT: G 186 ASN cc_start: 0.7389 (p0) cc_final: 0.6733 (p0) REVERT: G 187 LEU cc_start: 0.7927 (tp) cc_final: 0.7582 (tt) REVERT: G 286 THR cc_start: 0.7360 (p) cc_final: 0.7124 (t) REVERT: G 317 ASN cc_start: 0.7984 (m110) cc_final: 0.7643 (m-40) REVERT: G 364 ASP cc_start: 0.7276 (t70) cc_final: 0.6914 (t70) REVERT: G 453 TYR cc_start: 0.5703 (t80) cc_final: 0.5386 (t80) REVERT: G 478 LYS cc_start: 0.3780 (OUTLIER) cc_final: 0.3428 (tmmt) REVERT: G 493 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6278 (mmp-170) REVERT: G 546 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7459 (tt) REVERT: G 591 SER cc_start: 0.8439 (t) cc_final: 0.8223 (m) REVERT: G 655 TYR cc_start: 0.7871 (t80) cc_final: 0.7419 (t80) REVERT: G 764 LYS cc_start: 0.8065 (tttt) cc_final: 0.7861 (ttmm) REVERT: G 779 GLN cc_start: 0.7933 (tt0) cc_final: 0.7654 (tt0) REVERT: G 819 GLU cc_start: 0.7500 (mt-10) cc_final: 0.6967 (mt-10) REVERT: G 855 PHE cc_start: 0.8002 (m-10) cc_final: 0.7785 (m-80) REVERT: G 900 MET cc_start: 0.7643 (mmm) cc_final: 0.7405 (mmm) REVERT: G 949 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7662 (mm-40) REVERT: G 976 VAL cc_start: 0.8312 (t) cc_final: 0.8010 (m) REVERT: G 1017 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6700 (tm-30) REVERT: G 1072 GLU cc_start: 0.7657 (pm20) cc_final: 0.7360 (pm20) REVERT: G 1127 ASP cc_start: 0.6974 (m-30) cc_final: 0.6759 (m-30) outliers start: 180 outliers final: 148 residues processed: 636 average time/residue: 0.4331 time to fit residues: 428.3566 Evaluate side-chains 658 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 492 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 158 ARG Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 969 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 30 LYS Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 104 LYS Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 87 ASN Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 LYS Chi-restraints excluded: chain D residue 122 ASN Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 187 LEU Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 231 ILE Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 386 LYS Chi-restraints excluded: chain D residue 400 PHE Chi-restraints excluded: chain D residue 402 ILE Chi-restraints excluded: chain D residue 440 LYS Chi-restraints excluded: chain D residue 458 LYS Chi-restraints excluded: chain D residue 523 THR Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 588 THR Chi-restraints excluded: chain D residue 616 ASN Chi-restraints excluded: chain D residue 663 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 900 MET Chi-restraints excluded: chain D residue 947 LYS Chi-restraints excluded: chain D residue 969 LYS Chi-restraints excluded: chain D residue 1041 ASP Chi-restraints excluded: chain D residue 1077 THR Chi-restraints excluded: chain D residue 1100 THR Chi-restraints excluded: chain D residue 1104 VAL Chi-restraints excluded: chain D residue 1129 VAL Chi-restraints excluded: chain D residue 1141 LEU Chi-restraints excluded: chain E residue 1 GLU Chi-restraints excluded: chain E residue 52 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 195 VAL Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 161 VAL Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 197 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 47 VAL Chi-restraints excluded: chain G residue 62 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 99 ASN Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain G residue 128 ILE Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 171 VAL Chi-restraints excluded: chain G residue 229 LEU Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 281 GLU Chi-restraints excluded: chain G residue 323 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 351 TYR Chi-restraints excluded: chain G residue 375 PHE Chi-restraints excluded: chain G residue 383 SER Chi-restraints excluded: chain G residue 400 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 408 ARG Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 432 CYS Chi-restraints excluded: chain G residue 440 LYS Chi-restraints excluded: chain G residue 452 LEU Chi-restraints excluded: chain G residue 458 LYS Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 478 LYS Chi-restraints excluded: chain G residue 486 PHE Chi-restraints excluded: chain G residue 493 ARG Chi-restraints excluded: chain G residue 528 LYS Chi-restraints excluded: chain G residue 536 ASN Chi-restraints excluded: chain G residue 542 ASN Chi-restraints excluded: chain G residue 546 LEU Chi-restraints excluded: chain G residue 553 THR Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain G residue 588 THR Chi-restraints excluded: chain G residue 605 SER Chi-restraints excluded: chain G residue 660 TYR Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 746 SER Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 791 THR Chi-restraints excluded: chain G residue 935 GLN Chi-restraints excluded: chain G residue 947 LYS Chi-restraints excluded: chain G residue 950 ASP Chi-restraints excluded: chain G residue 975 SER Chi-restraints excluded: chain G residue 991 VAL Chi-restraints excluded: chain G residue 1041 ASP Chi-restraints excluded: chain G residue 1086 LYS Chi-restraints excluded: chain G residue 1116 THR Chi-restraints excluded: chain G residue 1136 THR Chi-restraints excluded: chain G residue 1141 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 8.9990 chunk 315 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 272 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 296 optimal weight: 0.0270 chunk 124 optimal weight: 0.8980 chunk 304 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 317 ASN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1101 HIS D 121 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 HIS ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 913 GLN F 110 GLN G 66 HIS ** G 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 314 GLN ** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 542 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.200589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.144943 restraints weight = 42199.664| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.11 r_work: 0.3524 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30124 Z= 0.190 Angle : 0.565 10.329 41029 Z= 0.287 Chirality : 0.044 0.246 4712 Planarity : 0.005 0.103 5285 Dihedral : 6.348 79.467 4705 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.49 % Favored : 90.46 % Rotamer: Outliers : 5.51 % Allowed : 19.11 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.48 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.14), residues: 3700 helix: 0.80 (0.22), residues: 649 sheet: -0.99 (0.17), residues: 870 loop : -2.31 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 64 HIS 0.003 0.001 HIS G1101 PHE 0.030 0.001 PHE D 106 TYR 0.027 0.001 TYR D 170 ARG 0.005 0.000 ARG D1019 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9111.26 seconds wall clock time: 163 minutes 51.99 seconds (9831.99 seconds total)