Starting phenix.real_space_refine on Fri May 30 00:56:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0k_37980/05_2025/8x0k_37980.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0k_37980/05_2025/8x0k_37980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x0k_37980/05_2025/8x0k_37980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0k_37980/05_2025/8x0k_37980.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0k_37980/05_2025/8x0k_37980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0k_37980/05_2025/8x0k_37980.cif" } resolution = 3.5 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= 0.008 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 260 5.16 5 C 20584 2.51 5 N 5668 2.21 5 O 6224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 32740 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1249 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3256 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "C" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 409} Chain: "E" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1249 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "F" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3256 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "G" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 409} Chain: "I" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1249 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "J" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3256 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "K" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 409} Chain: "M" Number of atoms: 1249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1249 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "N" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3256 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 31, 'TRANS': 386} Chain: "O" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 409} Chain: "D" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 280 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "H" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 280 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "L" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 280 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 280 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "O" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.48, per 1000 atoms: 0.53 Number of scatterers: 32740 At special positions: 0 Unit cell: (209, 191.4, 196.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 260 16.00 O 6224 8.00 N 5668 7.00 C 20584 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=68, symmetry=0 Simple disulfide: pdb=" SG CYS B 352 " - pdb=" SG CYS B 458 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 424 " - pdb=" SG CYS B 438 " distance=2.02 Simple disulfide: pdb=" SG CYS B 486 " - pdb=" SG CYS B 598 " distance=2.05 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 558 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 864 " - pdb=" SG CYS C 929 " distance=2.03 Simple disulfide: pdb=" SG CYS C 877 " - pdb=" SG CYS C 909 " distance=2.03 Simple disulfide: pdb=" SG CYS C 878 " - pdb=" SG CYS C 911 " distance=2.03 Simple disulfide: pdb=" SG CYS C 883 " - pdb=" SG CYS C 893 " distance=2.03 Simple disulfide: pdb=" SG CYS C1074 " - pdb=" SG CYS C1086 " distance=2.03 Simple disulfide: pdb=" SG CYS C1116 " - pdb=" SG CYS C1191 " distance=2.03 Simple disulfide: pdb=" SG CYS C1121 " - pdb=" SG CYS C1195 " distance=2.03 Simple disulfide: pdb=" SG CYS C1143 " - pdb=" SG CYS C1185 " distance=2.03 Simple disulfide: pdb=" SG CYS F 352 " - pdb=" SG CYS F 458 " distance=2.03 Simple disulfide: pdb=" SG CYS F 355 " - pdb=" SG CYS F 361 " distance=2.04 Simple disulfide: pdb=" SG CYS F 424 " - pdb=" SG CYS F 438 " distance=2.03 Simple disulfide: pdb=" SG CYS F 486 " - pdb=" SG CYS F 598 " distance=2.03 Simple disulfide: pdb=" SG CYS F 534 " - pdb=" SG CYS F 558 " distance=2.03 Simple disulfide: pdb=" SG CYS F 536 " - pdb=" SG CYS F 553 " distance=2.03 Simple disulfide: pdb=" SG CYS G 864 " - pdb=" SG CYS G 929 " distance=2.03 Simple disulfide: pdb=" SG CYS G 877 " - pdb=" SG CYS G 909 " distance=2.03 Simple disulfide: pdb=" SG CYS G 878 " - pdb=" SG CYS G 911 " distance=2.03 Simple disulfide: pdb=" SG CYS G 883 " - pdb=" SG CYS G 893 " distance=2.03 Simple disulfide: pdb=" SG CYS G1074 " - pdb=" SG CYS G1086 " distance=2.05 Simple disulfide: pdb=" SG CYS G1116 " - pdb=" SG CYS G1191 " distance=2.03 Simple disulfide: pdb=" SG CYS G1121 " - pdb=" SG CYS G1195 " distance=2.03 Simple disulfide: pdb=" SG CYS G1143 " - pdb=" SG CYS G1185 " distance=2.03 Simple disulfide: pdb=" SG CYS J 352 " - pdb=" SG CYS J 458 " distance=2.03 Simple disulfide: pdb=" SG CYS J 355 " - pdb=" SG CYS J 361 " distance=2.04 Simple disulfide: pdb=" SG CYS J 424 " - pdb=" SG CYS J 438 " distance=2.02 Simple disulfide: pdb=" SG CYS J 486 " - pdb=" SG CYS J 598 " distance=2.04 Simple disulfide: pdb=" SG CYS J 534 " - pdb=" SG CYS J 558 " distance=2.03 Simple disulfide: pdb=" SG CYS J 536 " - pdb=" SG CYS J 553 " distance=2.03 Simple disulfide: pdb=" SG CYS K 864 " - pdb=" SG CYS K 929 " distance=2.03 Simple disulfide: pdb=" SG CYS K 877 " - pdb=" SG CYS K 909 " distance=2.03 Simple disulfide: pdb=" SG CYS K 878 " - pdb=" SG CYS K 911 " distance=2.03 Simple disulfide: pdb=" SG CYS K 883 " - pdb=" SG CYS K 893 " distance=2.03 Simple disulfide: pdb=" SG CYS K1074 " - pdb=" SG CYS K1086 " distance=2.02 Simple disulfide: pdb=" SG CYS K1116 " - pdb=" SG CYS K1191 " distance=2.03 Simple disulfide: pdb=" SG CYS K1121 " - pdb=" SG CYS K1195 " distance=2.03 Simple disulfide: pdb=" SG CYS K1143 " - pdb=" SG CYS K1185 " distance=2.03 Simple disulfide: pdb=" SG CYS N 352 " - pdb=" SG CYS N 458 " distance=2.03 Simple disulfide: pdb=" SG CYS N 355 " - pdb=" SG CYS N 361 " distance=2.04 Simple disulfide: pdb=" SG CYS N 424 " - pdb=" SG CYS N 438 " distance=2.03 Simple disulfide: pdb=" SG CYS N 486 " - pdb=" SG CYS N 598 " distance=2.04 Simple disulfide: pdb=" SG CYS N 534 " - pdb=" SG CYS N 558 " distance=2.03 Simple disulfide: pdb=" SG CYS N 536 " - pdb=" SG CYS N 553 " distance=2.03 Simple disulfide: pdb=" SG CYS O 864 " - pdb=" SG CYS O 929 " distance=2.03 Simple disulfide: pdb=" SG CYS O 877 " - pdb=" SG CYS O 909 " distance=2.03 Simple disulfide: pdb=" SG CYS O 878 " - pdb=" SG CYS O 911 " distance=2.03 Simple disulfide: pdb=" SG CYS O 883 " - pdb=" SG CYS O 893 " distance=2.03 Simple disulfide: pdb=" SG CYS O1074 " - pdb=" SG CYS O1086 " distance=2.04 Simple disulfide: pdb=" SG CYS O1116 " - pdb=" SG CYS O1191 " distance=2.03 Simple disulfide: pdb=" SG CYS O1121 " - pdb=" SG CYS O1195 " distance=2.03 Simple disulfide: pdb=" SG CYS O1143 " - pdb=" SG CYS O1185 " distance=2.04 Simple disulfide: pdb=" SG CYS D 83 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 90 " - pdb=" SG CYS D 110 " distance=2.03 Simple disulfide: pdb=" SG CYS D 104 " - pdb=" SG CYS D 119 " distance=2.03 Simple disulfide: pdb=" SG CYS H 83 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 90 " - pdb=" SG CYS H 110 " distance=2.03 Simple disulfide: pdb=" SG CYS H 104 " - pdb=" SG CYS H 119 " distance=2.03 Simple disulfide: pdb=" SG CYS L 83 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 90 " - pdb=" SG CYS L 110 " distance=2.03 Simple disulfide: pdb=" SG CYS L 104 " - pdb=" SG CYS L 119 " distance=2.03 Simple disulfide: pdb=" SG CYS P 83 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS P 90 " - pdb=" SG CYS P 110 " distance=2.03 Simple disulfide: pdb=" SG CYS P 104 " - pdb=" SG CYS P 119 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG C1701 " - " ASN C 956 " " NAG G1701 " - " ASN G 956 " " NAG K1701 " - " ASN K 956 " " NAG O1701 " - " ASN O 956 " " NAG Q 1 " - " ASN B 533 " " NAG R 1 " - " ASN B 595 " " NAG S 1 " - " ASN F 533 " " NAG T 1 " - " ASN F 595 " " NAG U 1 " - " ASN J 533 " " NAG V 1 " - " ASN J 595 " " NAG W 1 " - " ASN N 533 " " NAG X 1 " - " ASN N 595 " Time building additional restraints: 7.45 Conformation dependent library (CDL) restraints added in 3.9 seconds 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7808 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 96 sheets defined 15.1% alpha, 38.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.88 Creating SS restraints... Processing helix chain 'A' and resid 106 through 119 removed outlier: 3.919A pdb=" N ASP A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.723A pdb=" N LEU A 158 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 178 removed outlier: 3.607A pdb=" N ARG A 178 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 345 removed outlier: 4.744A pdb=" N VAL B 341 " --> pdb=" O HIS B 338 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS B 343 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 554 through 556 No H-bonds generated for 'chain 'B' and resid 554 through 556' Processing helix chain 'B' and resid 683 through 695 Processing helix chain 'B' and resid 695 through 730 removed outlier: 3.571A pdb=" N THR B 699 " --> pdb=" O TYR B 695 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 748 Processing helix chain 'C' and resid 1053 through 1061 removed outlier: 3.511A pdb=" N TYR C1057 " --> pdb=" O SER C1053 " (cutoff:3.500A) Processing helix chain 'C' and resid 1065 through 1069 Processing helix chain 'C' and resid 1070 through 1074 removed outlier: 4.110A pdb=" N GLY C1073 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS C1074 " --> pdb=" O PRO C1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1070 through 1074' Processing helix chain 'C' and resid 1098 through 1102 removed outlier: 3.714A pdb=" N ALA C1101 " --> pdb=" O PRO C1098 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE C1102 " --> pdb=" O ASP C1099 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1098 through 1102' Processing helix chain 'C' and resid 1219 through 1253 removed outlier: 3.831A pdb=" N ARG C1253 " --> pdb=" O ILE C1249 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.926A pdb=" N ASP E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 178 removed outlier: 3.543A pdb=" N MET E 177 " --> pdb=" O PRO E 174 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG E 178 " --> pdb=" O VAL E 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 174 through 178' Processing helix chain 'F' and resid 336 through 345 removed outlier: 3.589A pdb=" N PHE F 339 " --> pdb=" O SER F 336 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL F 341 " --> pdb=" O HIS F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 416 No H-bonds generated for 'chain 'F' and resid 414 through 416' Processing helix chain 'F' and resid 554 through 556 No H-bonds generated for 'chain 'F' and resid 554 through 556' Processing helix chain 'F' and resid 683 through 695 Processing helix chain 'F' and resid 695 through 735 Proline residue: F 731 - end of helix removed outlier: 3.525A pdb=" N LEU F 734 " --> pdb=" O THR F 730 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR F 735 " --> pdb=" O PRO F 731 " (cutoff:3.500A) Processing helix chain 'F' and resid 741 through 748 Processing helix chain 'G' and resid 1053 through 1061 removed outlier: 3.546A pdb=" N TYR G1057 " --> pdb=" O SER G1053 " (cutoff:3.500A) Processing helix chain 'G' and resid 1065 through 1069 Processing helix chain 'G' and resid 1070 through 1074 removed outlier: 4.019A pdb=" N GLY G1073 " --> pdb=" O ALA G1070 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N CYS G1074 " --> pdb=" O PRO G1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1070 through 1074' Processing helix chain 'G' and resid 1098 through 1102 removed outlier: 3.708A pdb=" N ALA G1101 " --> pdb=" O PRO G1098 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE G1102 " --> pdb=" O ASP G1099 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1098 through 1102' Processing helix chain 'G' and resid 1219 through 1253 Processing helix chain 'I' and resid 107 through 119 Processing helix chain 'I' and resid 174 through 178 Processing helix chain 'J' and resid 335 through 345 removed outlier: 3.821A pdb=" N ASN J 340 " --> pdb=" O GLN J 337 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N VAL J 341 " --> pdb=" O HIS J 338 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR J 342 " --> pdb=" O PHE J 339 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR J 345 " --> pdb=" O TYR J 342 " (cutoff:3.500A) Processing helix chain 'J' and resid 414 through 416 No H-bonds generated for 'chain 'J' and resid 414 through 416' Processing helix chain 'J' and resid 554 through 556 No H-bonds generated for 'chain 'J' and resid 554 through 556' Processing helix chain 'J' and resid 683 through 695 Processing helix chain 'J' and resid 695 through 735 Proline residue: J 731 - end of helix removed outlier: 3.689A pdb=" N LEU J 734 " --> pdb=" O THR J 730 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR J 735 " --> pdb=" O PRO J 731 " (cutoff:3.500A) Processing helix chain 'J' and resid 741 through 748 Processing helix chain 'K' and resid 1053 through 1061 removed outlier: 3.586A pdb=" N TYR K1057 " --> pdb=" O SER K1053 " (cutoff:3.500A) Processing helix chain 'K' and resid 1065 through 1069 Processing helix chain 'K' and resid 1104 through 1108 removed outlier: 3.573A pdb=" N GLU K1107 " --> pdb=" O ARG K1104 " (cutoff:3.500A) Processing helix chain 'K' and resid 1219 through 1253 removed outlier: 3.513A pdb=" N ARG K1253 " --> pdb=" O ILE K1249 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 120 removed outlier: 3.613A pdb=" N ASP M 118 " --> pdb=" O LYS M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 153 through 158 removed outlier: 3.690A pdb=" N LYS M 157 " --> pdb=" O ALA M 153 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU M 158 " --> pdb=" O ASP M 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 153 through 158' Processing helix chain 'M' and resid 174 through 178 Processing helix chain 'N' and resid 335 through 345 removed outlier: 4.570A pdb=" N VAL N 341 " --> pdb=" O HIS N 338 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR N 345 " --> pdb=" O TYR N 342 " (cutoff:3.500A) Processing helix chain 'N' and resid 414 through 416 No H-bonds generated for 'chain 'N' and resid 414 through 416' Processing helix chain 'N' and resid 554 through 556 No H-bonds generated for 'chain 'N' and resid 554 through 556' Processing helix chain 'N' and resid 683 through 695 Processing helix chain 'N' and resid 695 through 735 Proline residue: N 731 - end of helix Processing helix chain 'N' and resid 741 through 748 Processing helix chain 'O' and resid 1053 through 1061 removed outlier: 3.583A pdb=" N TYR O1057 " --> pdb=" O SER O1053 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU O1061 " --> pdb=" O TYR O1057 " (cutoff:3.500A) Processing helix chain 'O' and resid 1065 through 1069 Processing helix chain 'O' and resid 1070 through 1074 removed outlier: 4.035A pdb=" N GLY O1073 " --> pdb=" O ALA O1070 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS O1074 " --> pdb=" O PRO O1071 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1070 through 1074' Processing helix chain 'O' and resid 1098 through 1102 removed outlier: 3.837A pdb=" N PHE O1102 " --> pdb=" O ASP O1099 " (cutoff:3.500A) Processing helix chain 'O' and resid 1219 through 1253 removed outlier: 3.701A pdb=" N ARG O1253 " --> pdb=" O ILE O1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'L' and resid 101 through 103 No H-bonds generated for 'chain 'L' and resid 101 through 103' Processing helix chain 'P' and resid 101 through 103 No H-bonds generated for 'chain 'P' and resid 101 through 103' Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 150 removed outlier: 4.298A pdb=" N GLY A 131 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS A 125 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N VAL A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR A 132 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 191 through 193 removed outlier: 5.200A pdb=" N PHE A 207 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 249 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 234 " --> pdb=" O VAL A 249 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.711A pdb=" N ILE A 223 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N VAL A 234 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 249 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 350 through 352 Processing sheet with id=AA5, first strand: chain 'B' and resid 367 through 371 removed outlier: 7.107A pdb=" N GLN B 382 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL B 370 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS B 380 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N SER B 384 " --> pdb=" O ALA B 403 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA B 403 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 386 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS B 399 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 367 through 371 removed outlier: 7.107A pdb=" N GLN B 382 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N VAL B 370 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LYS B 380 " --> pdb=" O VAL B 370 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 383 " --> pdb=" O HIS B 432 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS B 432 " --> pdb=" O PHE B 383 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N ALA B 385 " --> pdb=" O MET B 430 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N MET B 430 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 10.015A pdb=" N ILE B 387 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 11.307A pdb=" N GLY B 428 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 16.323A pdb=" N ILE B 389 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 19.081A pdb=" N VAL B 426 " --> pdb=" O ILE B 389 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 417 through 419 removed outlier: 4.476A pdb=" N GLU B 442 " --> pdb=" O TYR B 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 481 through 489 Processing sheet with id=AA9, first strand: chain 'B' and resid 569 through 570 Processing sheet with id=AB1, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.526A pdb=" N ASP B 510 " --> pdb=" O VAL B 560 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N VAL B 560 " --> pdb=" O ASP B 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 515 through 517 Processing sheet with id=AB3, first strand: chain 'B' and resid 607 through 609 Processing sheet with id=AB4, first strand: chain 'B' and resid 639 through 643 Processing sheet with id=AB5, first strand: chain 'C' and resid 817 through 823 Processing sheet with id=AB6, first strand: chain 'C' and resid 830 through 834 removed outlier: 6.773A pdb=" N LYS C 947 " --> pdb=" O VAL C 849 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N THR C 851 " --> pdb=" O LYS C 945 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS C 945 " --> pdb=" O THR C 851 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 830 through 834 Processing sheet with id=AB8, first strand: chain 'C' and resid 855 through 863 removed outlier: 6.667A pdb=" N ALA C 942 " --> pdb=" O PRO C 855 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU C 857 " --> pdb=" O HIS C 940 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N HIS C 940 " --> pdb=" O LEU C 857 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU C 859 " --> pdb=" O LYS C 938 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS C 938 " --> pdb=" O LEU C 859 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N TYR C 861 " --> pdb=" O ALA C 936 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 866 through 869 Processing sheet with id=AC1, first strand: chain 'C' and resid 866 through 869 Processing sheet with id=AC2, first strand: chain 'C' and resid 1018 through 1019 Processing sheet with id=AC3, first strand: chain 'C' and resid 1035 through 1036 Processing sheet with id=AC4, first strand: chain 'C' and resid 1112 through 1121 removed outlier: 7.060A pdb=" N LEU C1114 " --> pdb=" O LYS C1136 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N LYS C1136 " --> pdb=" O LEU C1114 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N CYS C1116 " --> pdb=" O THR C1134 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR C1134 " --> pdb=" O CYS C1116 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL C1118 " --> pdb=" O THR C1132 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR C1132 " --> pdb=" O VAL C1118 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C1120 " --> pdb=" O VAL C1130 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 1158 through 1161 Processing sheet with id=AC6, first strand: chain 'E' and resid 149 through 150 removed outlier: 6.518A pdb=" N PHE E 121 " --> pdb=" O TYR E 132 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR E 132 " --> pdb=" O PHE E 121 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL E 123 " --> pdb=" O THR E 130 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR E 132 " --> pdb=" O PRO E 143 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 257 through 259 removed outlier: 4.923A pdb=" N PHE E 207 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N ALA E 199 " --> pdb=" O PRO E 210 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 232 " --> pdb=" O ILE E 223 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY E 237 " --> pdb=" O GLU E 265 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 257 through 259 removed outlier: 7.113A pdb=" N VAL E 249 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL E 234 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY E 237 " --> pdb=" O GLU E 265 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 350 through 352 Processing sheet with id=AD1, first strand: chain 'F' and resid 367 through 371 removed outlier: 7.169A pdb=" N GLN F 382 " --> pdb=" O GLU F 368 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL F 370 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS F 380 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N SER F 384 " --> pdb=" O ALA F 403 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA F 403 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS F 399 " --> pdb=" O GLY F 388 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 367 through 371 removed outlier: 7.169A pdb=" N GLN F 382 " --> pdb=" O GLU F 368 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL F 370 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS F 380 " --> pdb=" O VAL F 370 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N HIS F 432 " --> pdb=" O PHE F 383 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N ALA F 385 " --> pdb=" O MET F 430 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N MET F 430 " --> pdb=" O ALA F 385 " (cutoff:3.500A) removed outlier: 9.709A pdb=" N ILE F 387 " --> pdb=" O GLY F 428 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N GLY F 428 " --> pdb=" O ILE F 387 " (cutoff:3.500A) removed outlier: 16.604A pdb=" N ILE F 389 " --> pdb=" O VAL F 426 " (cutoff:3.500A) removed outlier: 19.095A pdb=" N VAL F 426 " --> pdb=" O ILE F 389 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 417 through 419 removed outlier: 4.347A pdb=" N GLU F 442 " --> pdb=" O TYR F 462 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 482 through 489 Processing sheet with id=AD5, first strand: chain 'F' and resid 569 through 570 Processing sheet with id=AD6, first strand: chain 'F' and resid 508 through 509 Processing sheet with id=AD7, first strand: chain 'F' and resid 514 through 517 Processing sheet with id=AD8, first strand: chain 'F' and resid 607 through 611 Processing sheet with id=AD9, first strand: chain 'F' and resid 639 through 643 Processing sheet with id=AE1, first strand: chain 'G' and resid 817 through 823 Processing sheet with id=AE2, first strand: chain 'G' and resid 830 through 834 removed outlier: 5.264A pdb=" N MET G 846 " --> pdb=" O MET G 951 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N MET G 951 " --> pdb=" O MET G 846 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL G 848 " --> pdb=" O ARG G 949 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG G 949 " --> pdb=" O VAL G 848 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU G 850 " --> pdb=" O LYS G 947 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 830 through 834 Processing sheet with id=AE4, first strand: chain 'G' and resid 858 through 863 removed outlier: 6.169A pdb=" N LEU G 859 " --> pdb=" O LYS G 938 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LYS G 938 " --> pdb=" O LEU G 859 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR G 861 " --> pdb=" O ALA G 936 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 866 through 869 Processing sheet with id=AE6, first strand: chain 'G' and resid 866 through 869 Processing sheet with id=AE7, first strand: chain 'G' and resid 1018 through 1019 Processing sheet with id=AE8, first strand: chain 'G' and resid 1035 through 1036 Processing sheet with id=AE9, first strand: chain 'G' and resid 1112 through 1121 removed outlier: 5.652A pdb=" N ASP G1113 " --> pdb=" O LYS G1136 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS G1136 " --> pdb=" O ASP G1113 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL G1130 " --> pdb=" O ALA G1119 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id=AF2, first strand: chain 'I' and resid 149 through 150 removed outlier: 3.930A pdb=" N GLY I 131 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N TYR I 132 " --> pdb=" O PRO I 143 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 191 through 195 removed outlier: 9.146A pdb=" N ALA I 199 " --> pdb=" O PRO I 210 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N PHE I 207 " --> pdb=" O LEU I 246 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL I 249 " --> pdb=" O VAL I 234 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL I 234 " --> pdb=" O VAL I 249 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 222 through 224 removed outlier: 6.977A pdb=" N ILE I 223 " --> pdb=" O VAL I 231 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL I 234 " --> pdb=" O VAL I 249 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL I 249 " --> pdb=" O VAL I 234 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 350 through 352 Processing sheet with id=AF6, first strand: chain 'J' and resid 367 through 371 removed outlier: 7.101A pdb=" N GLN J 382 " --> pdb=" O GLU J 368 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL J 370 " --> pdb=" O LYS J 380 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS J 380 " --> pdb=" O VAL J 370 " (cutoff:3.500A) removed outlier: 9.949A pdb=" N SER J 384 " --> pdb=" O ALA J 403 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA J 403 " --> pdb=" O SER J 384 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY J 388 " --> pdb=" O LYS J 399 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS J 399 " --> pdb=" O GLY J 388 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 367 through 371 removed outlier: 7.101A pdb=" N GLN J 382 " --> pdb=" O GLU J 368 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL J 370 " --> pdb=" O LYS J 380 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LYS J 380 " --> pdb=" O VAL J 370 " (cutoff:3.500A) removed outlier: 10.389A pdb=" N ILE J 381 " --> pdb=" O LYS J 437 " (cutoff:3.500A) removed outlier: 10.413A pdb=" N LYS J 437 " --> pdb=" O ILE J 381 " (cutoff:3.500A) removed outlier: 11.972A pdb=" N PHE J 383 " --> pdb=" O LEU J 435 " (cutoff:3.500A) removed outlier: 10.762A pdb=" N LEU J 435 " --> pdb=" O PHE J 383 " (cutoff:3.500A) removed outlier: 9.297A pdb=" N ALA J 385 " --> pdb=" O PHE J 433 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N PHE J 433 " --> pdb=" O ALA J 385 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N ILE J 389 " --> pdb=" O THR J 429 " (cutoff:3.500A) removed outlier: 12.931A pdb=" N THR J 429 " --> pdb=" O ILE J 389 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 417 through 419 removed outlier: 4.363A pdb=" N GLU J 442 " --> pdb=" O TYR J 462 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 482 through 489 Processing sheet with id=AG1, first strand: chain 'J' and resid 569 through 570 Processing sheet with id=AG2, first strand: chain 'J' and resid 509 through 510 removed outlier: 3.639A pdb=" N ASP J 510 " --> pdb=" O VAL J 560 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL J 560 " --> pdb=" O ASP J 510 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 514 through 517 Processing sheet with id=AG4, first strand: chain 'J' and resid 607 through 609 Processing sheet with id=AG5, first strand: chain 'J' and resid 639 through 643 Processing sheet with id=AG6, first strand: chain 'K' and resid 817 through 823 Processing sheet with id=AG7, first strand: chain 'K' and resid 830 through 834 removed outlier: 5.406A pdb=" N MET K 846 " --> pdb=" O MET K 951 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N MET K 951 " --> pdb=" O MET K 846 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL K 848 " --> pdb=" O ARG K 949 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG K 949 " --> pdb=" O VAL K 848 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU K 850 " --> pdb=" O LYS K 947 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR K 856 " --> pdb=" O THR K 941 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N THR K 941 " --> pdb=" O THR K 856 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ASN K 858 " --> pdb=" O ALA K 939 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA K 939 " --> pdb=" O ASN K 858 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU K 860 " --> pdb=" O TYR K 937 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR K 937 " --> pdb=" O GLU K 860 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE K 862 " --> pdb=" O SER K 935 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER K 935 " --> pdb=" O ILE K 862 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 955 through 962 removed outlier: 6.733A pdb=" N SER K 935 " --> pdb=" O ILE K 862 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE K 862 " --> pdb=" O SER K 935 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N TYR K 937 " --> pdb=" O GLU K 860 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU K 860 " --> pdb=" O TYR K 937 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA K 939 " --> pdb=" O ASN K 858 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ASN K 858 " --> pdb=" O ALA K 939 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N THR K 941 " --> pdb=" O THR K 856 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR K 856 " --> pdb=" O THR K 941 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU K 850 " --> pdb=" O LYS K 947 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG K 949 " --> pdb=" O VAL K 848 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL K 848 " --> pdb=" O ARG K 949 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N MET K 951 " --> pdb=" O MET K 846 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N MET K 846 " --> pdb=" O MET K 951 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 866 through 869 Processing sheet with id=AH1, first strand: chain 'K' and resid 866 through 869 Processing sheet with id=AH2, first strand: chain 'K' and resid 902 through 903 Processing sheet with id=AH3, first strand: chain 'K' and resid 1018 through 1019 Processing sheet with id=AH4, first strand: chain 'K' and resid 1035 through 1036 Processing sheet with id=AH5, first strand: chain 'K' and resid 1112 through 1121 removed outlier: 7.400A pdb=" N LEU K1114 " --> pdb=" O LYS K1136 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N LYS K1136 " --> pdb=" O LEU K1114 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N CYS K1116 " --> pdb=" O THR K1134 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N THR K1134 " --> pdb=" O CYS K1116 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N VAL K1118 " --> pdb=" O THR K1132 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N THR K1132 " --> pdb=" O VAL K1118 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 1158 through 1161 Processing sheet with id=AH7, first strand: chain 'M' and resid 149 through 150 removed outlier: 3.959A pdb=" N GLY M 131 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS M 125 " --> pdb=" O VAL M 129 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N VAL M 129 " --> pdb=" O HIS M 125 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'M' and resid 191 through 193 removed outlier: 4.981A pdb=" N PHE M 207 " --> pdb=" O LEU M 246 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL M 249 " --> pdb=" O VAL M 234 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL M 234 " --> pdb=" O VAL M 249 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'M' and resid 222 through 224 removed outlier: 6.731A pdb=" N ILE M 223 " --> pdb=" O VAL M 231 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL M 234 " --> pdb=" O VAL M 249 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL M 249 " --> pdb=" O VAL M 234 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'N' and resid 350 through 352 Processing sheet with id=AI2, first strand: chain 'N' and resid 367 through 371 removed outlier: 7.059A pdb=" N GLN N 382 " --> pdb=" O GLU N 368 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL N 370 " --> pdb=" O LYS N 380 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS N 380 " --> pdb=" O VAL N 370 " (cutoff:3.500A) removed outlier: 27.618A pdb=" N LYS N 380 " --> pdb=" O ASP N 404 " (cutoff:3.500A) removed outlier: 22.914A pdb=" N ASP N 404 " --> pdb=" O LYS N 380 " (cutoff:3.500A) removed outlier: 16.983A pdb=" N GLN N 382 " --> pdb=" O TYR N 402 " (cutoff:3.500A) removed outlier: 14.057A pdb=" N TYR N 402 " --> pdb=" O GLN N 382 " (cutoff:3.500A) removed outlier: 12.025A pdb=" N SER N 384 " --> pdb=" O ILE N 400 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N ILE N 400 " --> pdb=" O SER N 384 " (cutoff:3.500A) removed outlier: 11.873A pdb=" N GLN N 386 " --> pdb=" O THR N 398 " (cutoff:3.500A) removed outlier: 9.867A pdb=" N THR N 398 " --> pdb=" O GLN N 386 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLY N 388 " --> pdb=" O ASP N 396 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'N' and resid 367 through 371 removed outlier: 7.059A pdb=" N GLN N 382 " --> pdb=" O GLU N 368 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N VAL N 370 " --> pdb=" O LYS N 380 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS N 380 " --> pdb=" O VAL N 370 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N HIS N 432 " --> pdb=" O PHE N 383 " (cutoff:3.500A) removed outlier: 9.752A pdb=" N ALA N 385 " --> pdb=" O MET N 430 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N MET N 430 " --> pdb=" O ALA N 385 " (cutoff:3.500A) removed outlier: 10.073A pdb=" N ILE N 387 " --> pdb=" O GLY N 428 " (cutoff:3.500A) removed outlier: 11.221A pdb=" N GLY N 428 " --> pdb=" O ILE N 387 " (cutoff:3.500A) removed outlier: 16.567A pdb=" N ILE N 389 " --> pdb=" O VAL N 426 " (cutoff:3.500A) removed outlier: 18.963A pdb=" N VAL N 426 " --> pdb=" O ILE N 389 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'N' and resid 417 through 419 removed outlier: 4.568A pdb=" N GLU N 442 " --> pdb=" O TYR N 462 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'N' and resid 482 through 483 Processing sheet with id=AI6, first strand: chain 'N' and resid 486 through 489 Processing sheet with id=AI7, first strand: chain 'N' and resid 499 through 502 Processing sheet with id=AI8, first strand: chain 'N' and resid 514 through 517 Processing sheet with id=AI9, first strand: chain 'N' and resid 541 through 544 Processing sheet with id=AJ1, first strand: chain 'N' and resid 607 through 611 removed outlier: 3.786A pdb=" N GLU N 614 " --> pdb=" O GLY N 611 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'N' and resid 639 through 643 Processing sheet with id=AJ3, first strand: chain 'O' and resid 817 through 823 Processing sheet with id=AJ4, first strand: chain 'O' and resid 830 through 834 removed outlier: 5.425A pdb=" N MET O 846 " --> pdb=" O MET O 951 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N MET O 951 " --> pdb=" O MET O 846 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL O 848 " --> pdb=" O ARG O 949 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG O 949 " --> pdb=" O VAL O 848 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU O 850 " --> pdb=" O LYS O 947 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR O 856 " --> pdb=" O THR O 941 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR O 941 " --> pdb=" O THR O 856 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASN O 858 " --> pdb=" O ALA O 939 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA O 939 " --> pdb=" O ASN O 858 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU O 860 " --> pdb=" O TYR O 937 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N TYR O 937 " --> pdb=" O GLU O 860 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE O 862 " --> pdb=" O SER O 935 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N SER O 935 " --> pdb=" O ILE O 862 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'O' and resid 955 through 962 removed outlier: 6.818A pdb=" N SER O 935 " --> pdb=" O ILE O 862 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE O 862 " --> pdb=" O SER O 935 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N TYR O 937 " --> pdb=" O GLU O 860 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLU O 860 " --> pdb=" O TYR O 937 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ALA O 939 " --> pdb=" O ASN O 858 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASN O 858 " --> pdb=" O ALA O 939 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR O 941 " --> pdb=" O THR O 856 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR O 856 " --> pdb=" O THR O 941 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU O 850 " --> pdb=" O LYS O 947 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG O 949 " --> pdb=" O VAL O 848 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N VAL O 848 " --> pdb=" O ARG O 949 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N MET O 951 " --> pdb=" O MET O 846 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N MET O 846 " --> pdb=" O MET O 951 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'O' and resid 866 through 869 Processing sheet with id=AJ7, first strand: chain 'O' and resid 866 through 869 Processing sheet with id=AJ8, first strand: chain 'O' and resid 1018 through 1019 Processing sheet with id=AJ9, first strand: chain 'O' and resid 1035 through 1036 Processing sheet with id=AK1, first strand: chain 'O' and resid 1112 through 1121 removed outlier: 5.840A pdb=" N ASP O1113 " --> pdb=" O LYS O1136 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LYS O1136 " --> pdb=" O ASP O1113 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL O1130 " --> pdb=" O ALA O1119 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'O' and resid 1158 through 1161 Processing sheet with id=AK3, first strand: chain 'D' and resid 87 through 89 Processing sheet with id=AK4, first strand: chain 'H' and resid 87 through 89 Processing sheet with id=AK5, first strand: chain 'L' and resid 87 through 89 Processing sheet with id=AK6, first strand: chain 'P' and resid 87 through 89 1310 hydrogen bonds defined for protein. 3279 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: 17.19 Time building geometry restraints manager: 8.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10702 1.35 - 1.48: 8605 1.48 - 1.61: 13924 1.61 - 1.74: 1 1.74 - 1.87: 348 Bond restraints: 33580 Sorted by residual: bond pdb=" CB PRO A 143 " pdb=" CG PRO A 143 " ideal model delta sigma weight residual 1.492 1.616 -0.124 5.00e-02 4.00e+02 6.13e+00 bond pdb=" CB CYS G1086 " pdb=" SG CYS G1086 " ideal model delta sigma weight residual 1.808 1.872 -0.064 3.30e-02 9.18e+02 3.77e+00 bond pdb=" C1 NAG G1701 " pdb=" O5 NAG G1701 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" CB PRO E 189 " pdb=" CG PRO E 189 " ideal model delta sigma weight residual 1.492 1.585 -0.093 5.00e-02 4.00e+02 3.45e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.25e+00 ... (remaining 33575 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 45305 2.98 - 5.96: 348 5.96 - 8.94: 38 8.94 - 11.92: 12 11.92 - 14.90: 1 Bond angle restraints: 45704 Sorted by residual: angle pdb=" CA PRO A 143 " pdb=" N PRO A 143 " pdb=" CD PRO A 143 " ideal model delta sigma weight residual 112.00 97.10 14.90 1.40e+00 5.10e-01 1.13e+02 angle pdb=" CA PRO B 731 " pdb=" N PRO B 731 " pdb=" CD PRO B 731 " ideal model delta sigma weight residual 112.00 102.45 9.55 1.40e+00 5.10e-01 4.65e+01 angle pdb=" C HIS J 503 " pdb=" N MET J 504 " pdb=" CA MET J 504 " ideal model delta sigma weight residual 121.20 129.80 -8.60 1.40e+00 5.10e-01 3.77e+01 angle pdb=" CA LYS N 529 " pdb=" CB LYS N 529 " pdb=" CG LYS N 529 " ideal model delta sigma weight residual 114.10 125.80 -11.70 2.00e+00 2.50e-01 3.42e+01 angle pdb=" CA PRO E 189 " pdb=" N PRO E 189 " pdb=" CD PRO E 189 " ideal model delta sigma weight residual 112.00 104.32 7.68 1.40e+00 5.10e-01 3.01e+01 ... (remaining 45699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 17223 17.87 - 35.75: 2444 35.75 - 53.62: 658 53.62 - 71.50: 95 71.50 - 89.37: 40 Dihedral angle restraints: 20460 sinusoidal: 8272 harmonic: 12188 Sorted by residual: dihedral pdb=" CB CYS F 355 " pdb=" SG CYS F 355 " pdb=" SG CYS F 361 " pdb=" CB CYS F 361 " ideal model delta sinusoidal sigma weight residual 93.00 163.58 -70.58 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CB CYS B 424 " pdb=" SG CYS B 424 " pdb=" SG CYS B 438 " pdb=" CB CYS B 438 " ideal model delta sinusoidal sigma weight residual 93.00 158.97 -65.97 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS O 883 " pdb=" SG CYS O 883 " pdb=" SG CYS O 893 " pdb=" CB CYS O 893 " ideal model delta sinusoidal sigma weight residual -86.00 -147.28 61.28 1 1.00e+01 1.00e-02 4.99e+01 ... (remaining 20457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 5103 0.154 - 0.308: 18 0.308 - 0.461: 0 0.461 - 0.615: 0 0.615 - 0.769: 3 Chirality restraints: 5124 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN F 595 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.63 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN N 595 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 595 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.54e+00 ... (remaining 5121 not shown) Planarity restraints: 5900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 142 " 0.102 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO A 143 " -0.244 5.00e-02 4.00e+02 pdb=" CA PRO A 143 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO A 143 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 188 " 0.092 5.00e-02 4.00e+02 1.35e-01 2.93e+01 pdb=" N PRO E 189 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO E 189 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO E 189 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 346 " -0.075 5.00e-02 4.00e+02 1.13e-01 2.05e+01 pdb=" N PRO B 347 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO B 347 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO B 347 " -0.060 5.00e-02 4.00e+02 ... (remaining 5897 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 443 2.63 - 3.19: 27949 3.19 - 3.76: 47261 3.76 - 4.33: 60728 4.33 - 4.90: 104809 Nonbonded interactions: 241190 Sorted by model distance: nonbonded pdb=" OH TYR N 402 " pdb=" OD1 ASP N 450 " model vdw 2.058 3.040 nonbonded pdb=" OD2 ASP L 115 " pdb="CA CA L 400 " model vdw 2.079 2.510 nonbonded pdb=" OH TYR F 402 " pdb=" OD1 ASP F 450 " model vdw 2.084 3.040 nonbonded pdb=" O PRO E 189 " pdb=" OH TYR E 193 " model vdw 2.089 3.040 nonbonded pdb=" OE1 GLU N 373 " pdb=" OH TYR N 489 " model vdw 2.108 3.040 ... (remaining 241185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.200 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 73.860 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.210 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.004 0.124 33668 Z= 0.187 Angle : 0.752 19.849 45900 Z= 0.391 Chirality : 0.048 0.769 5124 Planarity : 0.006 0.141 5888 Dihedral : 17.184 89.372 12448 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.20 % Favored : 95.75 % Rotamer: Outliers : 0.73 % Allowed : 36.93 % Favored : 62.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.30 (0.13), residues: 4188 helix: 2.98 (0.24), residues: 432 sheet: 0.21 (0.15), residues: 1272 loop : -1.04 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP E 195 HIS 0.009 0.001 HIS B 395 PHE 0.031 0.002 PHE C1235 TYR 0.021 0.002 TYR J 692 ARG 0.009 0.001 ARG K 949 Details of bonding type rmsd link_NAG-ASN : bond 0.01461 ( 12) link_NAG-ASN : angle 6.73645 ( 36) link_BETA1-4 : bond 0.00460 ( 8) link_BETA1-4 : angle 2.19196 ( 24) hydrogen bonds : bond 0.11916 ( 1245) hydrogen bonds : angle 5.42938 ( 3279) SS BOND : bond 0.00452 ( 68) SS BOND : angle 1.98136 ( 136) covalent geometry : bond 0.00420 (33580) covalent geometry : angle 0.71945 (45704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 996 time to evaluate : 3.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 LYS cc_start: 0.8216 (tmmt) cc_final: 0.7821 (ttpp) REVERT: A 149 VAL cc_start: 0.8186 (t) cc_final: 0.7875 (p) REVERT: B 490 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7330 (mm110) REVERT: B 499 GLU cc_start: 0.7366 (pt0) cc_final: 0.6899 (pt0) REVERT: B 502 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7155 (mtp) REVERT: B 511 ARG cc_start: 0.8666 (tpp80) cc_final: 0.8437 (tpp80) REVERT: B 669 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7941 (mtt180) REVERT: F 679 LYS cc_start: 0.8295 (mmmt) cc_final: 0.8049 (mmmt) REVERT: G 894 LYS cc_start: 0.7872 (mmtp) cc_final: 0.7600 (mmtp) REVERT: G 1035 LYS cc_start: 0.7981 (ttpp) cc_final: 0.7753 (ttmm) REVERT: I 142 LYS cc_start: 0.8303 (tmmt) cc_final: 0.7888 (tmmt) REVERT: J 679 LYS cc_start: 0.8164 (mmtm) cc_final: 0.7794 (mttm) REVERT: K 1019 GLN cc_start: 0.8009 (mt0) cc_final: 0.7799 (mt0) REVERT: K 1074 CYS cc_start: 0.5907 (m) cc_final: 0.5694 (m) REVERT: N 399 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7746 (mtpp) REVERT: N 410 ASN cc_start: 0.8176 (m-40) cc_final: 0.7667 (m-40) REVERT: N 459 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7346 (ptm160) REVERT: N 534 CYS cc_start: 0.6288 (m) cc_final: 0.6033 (m) REVERT: O 920 GLU cc_start: 0.7614 (pm20) cc_final: 0.7354 (pm20) REVERT: O 1134 THR cc_start: 0.8511 (t) cc_final: 0.8259 (p) REVERT: O 1199 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7997 (mmmt) outliers start: 26 outliers final: 18 residues processed: 1003 average time/residue: 0.4624 time to fit residues: 721.7995 Evaluate side-chains 1011 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 992 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain B residue 376 ASP Chi-restraints excluded: chain B residue 502 MET Chi-restraints excluded: chain C residue 912 ASP Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 547 ASP Chi-restraints excluded: chain G residue 951 MET Chi-restraints excluded: chain G residue 1142 ASP Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain K residue 844 LEU Chi-restraints excluded: chain K residue 1142 ASP Chi-restraints excluded: chain K residue 1196 GLU Chi-restraints excluded: chain M residue 215 LYS Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain N residue 492 THR Chi-restraints excluded: chain N residue 623 HIS Chi-restraints excluded: chain N residue 658 MET Chi-restraints excluded: chain N residue 712 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 347 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 173 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 322 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 196 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 374 optimal weight: 5.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 964 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 HIS F 386 GLN F 461 GLN F 686 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 201 GLN J 337 GLN J 340 ASN J 559 HIS K 931 HIS K1090 ASN ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 689 GLN O 917 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.118716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100264 restraints weight = 54604.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.103475 restraints weight = 23268.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105528 restraints weight = 12584.634| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.0633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 33668 Z= 0.134 Angle : 0.613 18.836 45900 Z= 0.307 Chirality : 0.046 0.590 5124 Planarity : 0.005 0.083 5888 Dihedral : 5.732 63.256 5007 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.94 % Favored : 96.04 % Rotamer: Outliers : 4.55 % Allowed : 30.50 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.28 (0.13), residues: 4188 helix: 3.03 (0.23), residues: 432 sheet: 0.33 (0.15), residues: 1200 loop : -1.07 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 195 HIS 0.009 0.001 HIS J 559 PHE 0.012 0.001 PHE A 224 TYR 0.014 0.001 TYR G1057 ARG 0.007 0.001 ARG K 949 Details of bonding type rmsd link_NAG-ASN : bond 0.01434 ( 12) link_NAG-ASN : angle 6.25751 ( 36) link_BETA1-4 : bond 0.00391 ( 8) link_BETA1-4 : angle 1.27236 ( 24) hydrogen bonds : bond 0.03987 ( 1245) hydrogen bonds : angle 4.77179 ( 3279) SS BOND : bond 0.00313 ( 68) SS BOND : angle 1.22301 ( 136) covalent geometry : bond 0.00309 (33580) covalent geometry : angle 0.58464 (45704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 1036 time to evaluate : 3.583 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: A 149 VAL cc_start: 0.8465 (t) cc_final: 0.8198 (p) REVERT: B 490 GLN cc_start: 0.7678 (mm110) cc_final: 0.7371 (mm110) REVERT: B 499 GLU cc_start: 0.7356 (pt0) cc_final: 0.6900 (pt0) REVERT: B 502 MET cc_start: 0.7413 (mtp) cc_final: 0.7188 (mtp) REVERT: B 511 ARG cc_start: 0.8672 (tpp80) cc_final: 0.8414 (tpp80) REVERT: B 532 TYR cc_start: 0.8022 (p90) cc_final: 0.7514 (p90) REVERT: B 594 ASP cc_start: 0.7382 (t0) cc_final: 0.6933 (t0) REVERT: B 602 MET cc_start: 0.7828 (mtp) cc_final: 0.7582 (mtt) REVERT: B 669 ARG cc_start: 0.8311 (mtp85) cc_final: 0.7845 (mtt180) REVERT: C 904 TRP cc_start: 0.8627 (p-90) cc_final: 0.8340 (p-90) REVERT: C 1242 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7773 (p) REVERT: F 408 ILE cc_start: 0.8144 (mp) cc_final: 0.7862 (mm) REVERT: G 866 TYR cc_start: 0.7671 (p90) cc_final: 0.7371 (p90) REVERT: G 903 MET cc_start: 0.7669 (ttm) cc_final: 0.7255 (mtp) REVERT: G 1120 THR cc_start: 0.8091 (m) cc_final: 0.7656 (p) REVERT: I 243 ARG cc_start: 0.7406 (mmm-85) cc_final: 0.7163 (mmm-85) REVERT: J 396 ASP cc_start: 0.8069 (t0) cc_final: 0.6939 (t0) REVERT: J 399 LYS cc_start: 0.8407 (mtpp) cc_final: 0.7653 (mtmm) REVERT: J 449 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8069 (mt0) REVERT: J 490 GLN cc_start: 0.7436 (tp-100) cc_final: 0.7180 (tp-100) REVERT: J 515 SER cc_start: 0.7306 (OUTLIER) cc_final: 0.7094 (p) REVERT: J 679 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7727 (mttm) REVERT: K 903 MET cc_start: 0.7777 (mtp) cc_final: 0.7554 (mtp) REVERT: K 1074 CYS cc_start: 0.5968 (m) cc_final: 0.5672 (m) REVERT: K 1253 ARG cc_start: 0.5613 (OUTLIER) cc_final: 0.5346 (mtt180) REVERT: M 167 ASP cc_start: 0.7904 (t0) cc_final: 0.7617 (t0) REVERT: N 399 LYS cc_start: 0.7962 (mtpp) cc_final: 0.7595 (mtpp) REVERT: N 401 ARG cc_start: 0.8232 (ptt90) cc_final: 0.8004 (ptt180) REVERT: N 410 ASN cc_start: 0.7907 (m-40) cc_final: 0.7507 (m-40) REVERT: N 442 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7034 (mm-30) REVERT: N 529 LYS cc_start: 0.8026 (tptp) cc_final: 0.7794 (tptp) REVERT: N 557 GLN cc_start: 0.7852 (mt0) cc_final: 0.7591 (mp10) REVERT: N 653 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8624 (m) REVERT: O 920 GLU cc_start: 0.7732 (pm20) cc_final: 0.7424 (pm20) REVERT: O 1043 MET cc_start: 0.7289 (mmm) cc_final: 0.6894 (mmm) REVERT: O 1199 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7893 (mmmt) outliers start: 163 outliers final: 101 residues processed: 1120 average time/residue: 0.4515 time to fit residues: 789.4738 Evaluate side-chains 1113 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 1008 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain C residue 1153 THR Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 543 THR Chi-restraints excluded: chain F residue 561 SER Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 713 SER Chi-restraints excluded: chain G residue 862 ILE Chi-restraints excluded: chain G residue 951 MET Chi-restraints excluded: chain G residue 1002 GLN Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1059 LEU Chi-restraints excluded: chain G residue 1114 LEU Chi-restraints excluded: chain G residue 1158 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1222 LEU Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 251 TRP Chi-restraints excluded: chain J residue 361 CYS Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 420 THR Chi-restraints excluded: chain J residue 467 GLN Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 498 GLU Chi-restraints excluded: chain J residue 515 SER Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 653 VAL Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 ILE Chi-restraints excluded: chain J residue 718 CYS Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain J residue 744 LEU Chi-restraints excluded: chain K residue 821 VAL Chi-restraints excluded: chain K residue 960 ASP Chi-restraints excluded: chain K residue 961 VAL Chi-restraints excluded: chain K residue 1040 SER Chi-restraints excluded: chain K residue 1046 VAL Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1097 LEU Chi-restraints excluded: chain K residue 1105 ILE Chi-restraints excluded: chain K residue 1117 THR Chi-restraints excluded: chain K residue 1142 ASP Chi-restraints excluded: chain K residue 1232 LEU Chi-restraints excluded: chain K residue 1253 ARG Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 250 THR Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 496 THR Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain N residue 623 HIS Chi-restraints excluded: chain N residue 653 VAL Chi-restraints excluded: chain N residue 718 CYS Chi-restraints excluded: chain N residue 743 THR Chi-restraints excluded: chain N residue 747 LEU Chi-restraints excluded: chain O residue 875 VAL Chi-restraints excluded: chain O residue 923 VAL Chi-restraints excluded: chain O residue 951 MET Chi-restraints excluded: chain O residue 996 LYS Chi-restraints excluded: chain O residue 1075 GLN Chi-restraints excluded: chain O residue 1105 ILE Chi-restraints excluded: chain O residue 1115 THR Chi-restraints excluded: chain O residue 1151 VAL Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1244 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 180 optimal weight: 0.9990 chunk 376 optimal weight: 0.0980 chunk 189 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 253 optimal weight: 9.9990 chunk 238 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 HIS B 665 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN F 686 GLN G 833 HIS G1155 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS N 673 GLN N 686 GLN N 689 GLN O 917 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.119862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101339 restraints weight = 54993.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104553 restraints weight = 23401.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106609 restraints weight = 12576.213| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.0929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 33668 Z= 0.105 Angle : 0.590 18.693 45900 Z= 0.293 Chirality : 0.045 0.553 5124 Planarity : 0.004 0.067 5888 Dihedral : 5.041 55.648 4973 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 4.75 % Allowed : 30.39 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.21 (0.13), residues: 4188 helix: 3.04 (0.23), residues: 432 sheet: 0.36 (0.15), residues: 1232 loop : -1.01 (0.12), residues: 2524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 195 HIS 0.008 0.001 HIS J 559 PHE 0.008 0.001 PHE N 715 TYR 0.023 0.001 TYR C1057 ARG 0.006 0.000 ARG K 949 Details of bonding type rmsd link_NAG-ASN : bond 0.01375 ( 12) link_NAG-ASN : angle 6.06946 ( 36) link_BETA1-4 : bond 0.00403 ( 8) link_BETA1-4 : angle 1.40639 ( 24) hydrogen bonds : bond 0.03527 ( 1245) hydrogen bonds : angle 4.59241 ( 3279) SS BOND : bond 0.00286 ( 68) SS BOND : angle 1.34791 ( 136) covalent geometry : bond 0.00239 (33580) covalent geometry : angle 0.56075 (45704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1189 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 1019 time to evaluate : 3.512 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 135 LEU cc_start: 0.8401 (mp) cc_final: 0.8093 (mp) REVERT: A 149 VAL cc_start: 0.8505 (t) cc_final: 0.8234 (p) REVERT: A 249 VAL cc_start: 0.8516 (m) cc_final: 0.8104 (p) REVERT: B 399 LYS cc_start: 0.8421 (mtpp) cc_final: 0.8198 (mtpp) REVERT: B 401 ARG cc_start: 0.8381 (ptt180) cc_final: 0.7801 (ptt180) REVERT: B 490 GLN cc_start: 0.7676 (mm110) cc_final: 0.7400 (mm110) REVERT: B 502 MET cc_start: 0.7389 (mtp) cc_final: 0.7158 (mtp) REVERT: B 532 TYR cc_start: 0.7973 (p90) cc_final: 0.7453 (p90) REVERT: B 543 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7838 (m) REVERT: B 594 ASP cc_start: 0.7362 (t0) cc_final: 0.6945 (t0) REVERT: B 602 MET cc_start: 0.7752 (mtp) cc_final: 0.7495 (mtt) REVERT: B 669 ARG cc_start: 0.8203 (mtp85) cc_final: 0.7838 (mtt180) REVERT: B 690 TYR cc_start: 0.8605 (t80) cc_final: 0.8050 (t80) REVERT: C 904 TRP cc_start: 0.8626 (p-90) cc_final: 0.8355 (p-90) REVERT: C 1242 VAL cc_start: 0.8042 (OUTLIER) cc_final: 0.7809 (p) REVERT: F 408 ILE cc_start: 0.8369 (mp) cc_final: 0.8109 (mm) REVERT: F 430 MET cc_start: 0.7371 (tmm) cc_final: 0.6445 (tmm) REVERT: F 499 GLU cc_start: 0.7611 (pm20) cc_final: 0.7345 (pm20) REVERT: F 522 LYS cc_start: 0.8025 (tptt) cc_final: 0.7371 (tptt) REVERT: F 594 ASP cc_start: 0.7413 (t0) cc_final: 0.7213 (t0) REVERT: F 679 LYS cc_start: 0.8241 (mmmt) cc_final: 0.7954 (mmmt) REVERT: G 1009 SER cc_start: 0.8662 (t) cc_final: 0.8453 (t) REVERT: G 1029 TYR cc_start: 0.8011 (t80) cc_final: 0.7725 (t80) REVERT: G 1120 THR cc_start: 0.8083 (m) cc_final: 0.7647 (p) REVERT: I 142 LYS cc_start: 0.8383 (tmmt) cc_final: 0.7586 (tmmt) REVERT: I 243 ARG cc_start: 0.7379 (mmm-85) cc_final: 0.7145 (mmm-85) REVERT: J 378 MET cc_start: 0.7877 (mmm) cc_final: 0.7066 (mmm) REVERT: J 393 ASP cc_start: 0.6929 (t0) cc_final: 0.6197 (t70) REVERT: J 396 ASP cc_start: 0.7909 (t0) cc_final: 0.6811 (t0) REVERT: J 399 LYS cc_start: 0.8421 (mtpp) cc_final: 0.7630 (mtmm) REVERT: J 449 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8075 (mt0) REVERT: J 490 GLN cc_start: 0.7477 (tp-100) cc_final: 0.7095 (tp-100) REVERT: J 515 SER cc_start: 0.7243 (OUTLIER) cc_final: 0.7036 (p) REVERT: J 679 LYS cc_start: 0.8116 (mmtm) cc_final: 0.7732 (mttm) REVERT: J 718 CYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8218 (t) REVERT: K 903 MET cc_start: 0.7746 (mtp) cc_final: 0.7508 (mtp) REVERT: K 1074 CYS cc_start: 0.6054 (m) cc_final: 0.5800 (m) REVERT: K 1093 VAL cc_start: 0.8843 (p) cc_final: 0.8638 (p) REVERT: K 1253 ARG cc_start: 0.5576 (OUTLIER) cc_final: 0.5309 (mtt180) REVERT: M 167 ASP cc_start: 0.7924 (t0) cc_final: 0.7518 (t0) REVERT: M 188 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8479 (ttmm) REVERT: M 195 TRP cc_start: 0.8564 (t60) cc_final: 0.8115 (t60) REVERT: M 197 HIS cc_start: 0.8082 (m170) cc_final: 0.7614 (m170) REVERT: N 409 GLU cc_start: 0.7516 (mp0) cc_final: 0.7118 (mp0) REVERT: N 442 GLU cc_start: 0.7342 (mm-30) cc_final: 0.7074 (mm-30) REVERT: N 459 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7831 (ttm-80) REVERT: N 510 ASP cc_start: 0.8686 (t0) cc_final: 0.8473 (t0) REVERT: N 529 LYS cc_start: 0.8041 (tptp) cc_final: 0.7661 (tptp) REVERT: N 557 GLN cc_start: 0.7685 (mt0) cc_final: 0.7165 (tt0) REVERT: N 653 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8478 (m) REVERT: N 690 TYR cc_start: 0.8604 (t80) cc_final: 0.8373 (t80) REVERT: O 915 ASN cc_start: 0.8681 (m-40) cc_final: 0.8420 (m-40) REVERT: O 920 GLU cc_start: 0.7688 (pm20) cc_final: 0.7403 (pm20) REVERT: O 1199 LYS cc_start: 0.8267 (mmmt) cc_final: 0.7918 (mmmt) REVERT: O 1235 PHE cc_start: 0.8212 (t80) cc_final: 0.7911 (t80) outliers start: 170 outliers final: 114 residues processed: 1104 average time/residue: 0.4516 time to fit residues: 778.0357 Evaluate side-chains 1110 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 990 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain C residue 1153 THR Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 569 GLN Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 658 MET Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 691 TYR Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 713 SER Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1059 LEU Chi-restraints excluded: chain G residue 1114 LEU Chi-restraints excluded: chain G residue 1144 SER Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1214 PHE Chi-restraints excluded: chain G residue 1241 LEU Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 251 TRP Chi-restraints excluded: chain J residue 361 CYS Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 420 THR Chi-restraints excluded: chain J residue 467 GLN Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 498 GLU Chi-restraints excluded: chain J residue 508 THR Chi-restraints excluded: chain J residue 515 SER Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 551 ASN Chi-restraints excluded: chain J residue 572 SER Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 653 VAL Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 ILE Chi-restraints excluded: chain J residue 718 CYS Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain K residue 821 VAL Chi-restraints excluded: chain K residue 960 ASP Chi-restraints excluded: chain K residue 961 VAL Chi-restraints excluded: chain K residue 1040 SER Chi-restraints excluded: chain K residue 1046 VAL Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1097 LEU Chi-restraints excluded: chain K residue 1117 THR Chi-restraints excluded: chain K residue 1232 LEU Chi-restraints excluded: chain K residue 1253 ARG Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 469 VAL Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 560 VAL Chi-restraints excluded: chain N residue 623 HIS Chi-restraints excluded: chain N residue 653 VAL Chi-restraints excluded: chain N residue 743 THR Chi-restraints excluded: chain N residue 747 LEU Chi-restraints excluded: chain O residue 923 VAL Chi-restraints excluded: chain O residue 996 LYS Chi-restraints excluded: chain O residue 1024 GLU Chi-restraints excluded: chain O residue 1075 GLN Chi-restraints excluded: chain O residue 1105 ILE Chi-restraints excluded: chain O residue 1115 THR Chi-restraints excluded: chain O residue 1151 VAL Chi-restraints excluded: chain O residue 1156 GLU Chi-restraints excluded: chain O residue 1185 CYS Chi-restraints excluded: chain O residue 1244 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 31 optimal weight: 8.9990 chunk 331 optimal weight: 0.0670 chunk 304 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 399 optimal weight: 4.9990 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1001 ASN G1079 ASN I 172 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 467 GLN J 559 HIS K1075 GLN K1090 ASN O 917 GLN O 964 ASN O1226 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.119904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.101419 restraints weight = 54773.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104650 restraints weight = 23300.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106653 restraints weight = 12552.877| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 33668 Z= 0.105 Angle : 0.579 18.589 45900 Z= 0.286 Chirality : 0.045 0.551 5124 Planarity : 0.004 0.060 5888 Dihedral : 4.669 48.403 4966 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.39 % Rotamer: Outliers : 5.11 % Allowed : 29.78 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.15 (0.13), residues: 4188 helix: 3.02 (0.23), residues: 432 sheet: 0.45 (0.15), residues: 1224 loop : -0.99 (0.12), residues: 2532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 195 HIS 0.009 0.001 HIS J 559 PHE 0.012 0.001 PHE A 224 TYR 0.017 0.001 TYR C1057 ARG 0.009 0.000 ARG G 930 Details of bonding type rmsd link_NAG-ASN : bond 0.01411 ( 12) link_NAG-ASN : angle 6.18260 ( 36) link_BETA1-4 : bond 0.00419 ( 8) link_BETA1-4 : angle 1.40518 ( 24) hydrogen bonds : bond 0.03418 ( 1245) hydrogen bonds : angle 4.48874 ( 3279) SS BOND : bond 0.00269 ( 68) SS BOND : angle 1.22720 ( 136) covalent geometry : bond 0.00242 (33580) covalent geometry : angle 0.54901 (45704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 1008 time to evaluate : 3.463 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 135 LEU cc_start: 0.8304 (mp) cc_final: 0.7990 (mp) REVERT: A 149 VAL cc_start: 0.8528 (t) cc_final: 0.8266 (p) REVERT: A 249 VAL cc_start: 0.8499 (m) cc_final: 0.8071 (p) REVERT: B 354 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.7013 (t70) REVERT: B 399 LYS cc_start: 0.8413 (mtpp) cc_final: 0.8189 (mtpp) REVERT: B 490 GLN cc_start: 0.7645 (mm110) cc_final: 0.7357 (mm110) REVERT: B 502 MET cc_start: 0.7393 (mtp) cc_final: 0.7159 (mtp) REVERT: B 532 TYR cc_start: 0.7890 (p90) cc_final: 0.7391 (p90) REVERT: B 543 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7771 (m) REVERT: B 594 ASP cc_start: 0.7302 (t0) cc_final: 0.6871 (t0) REVERT: B 690 TYR cc_start: 0.8623 (t80) cc_final: 0.8041 (t80) REVERT: C 894 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7794 (mmmm) REVERT: C 904 TRP cc_start: 0.8639 (p-90) cc_final: 0.8364 (p-90) REVERT: C 930 ARG cc_start: 0.8467 (ttp-110) cc_final: 0.8236 (ttp80) REVERT: C 1014 ARG cc_start: 0.8627 (mmt180) cc_final: 0.8360 (mmt180) REVERT: C 1242 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7728 (p) REVERT: F 408 ILE cc_start: 0.8371 (mp) cc_final: 0.8107 (mm) REVERT: F 430 MET cc_start: 0.7371 (tmm) cc_final: 0.6621 (tmm) REVERT: F 499 GLU cc_start: 0.7598 (pm20) cc_final: 0.7338 (pm20) REVERT: F 594 ASP cc_start: 0.7425 (t0) cc_final: 0.7179 (t0) REVERT: F 679 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7915 (mmmt) REVERT: G 903 MET cc_start: 0.7661 (ttm) cc_final: 0.7217 (mtp) REVERT: G 1029 TYR cc_start: 0.8052 (t80) cc_final: 0.7773 (t80) REVERT: G 1120 THR cc_start: 0.8101 (m) cc_final: 0.7695 (p) REVERT: I 142 LYS cc_start: 0.8391 (tmmt) cc_final: 0.7556 (tmmt) REVERT: J 378 MET cc_start: 0.7828 (mmm) cc_final: 0.7032 (mmm) REVERT: J 393 ASP cc_start: 0.7010 (t0) cc_final: 0.6308 (t70) REVERT: J 396 ASP cc_start: 0.7888 (t0) cc_final: 0.6802 (t0) REVERT: J 399 LYS cc_start: 0.8446 (mtpp) cc_final: 0.7636 (mtmm) REVERT: J 490 GLN cc_start: 0.7516 (tp-100) cc_final: 0.7126 (tp-100) REVERT: J 502 MET cc_start: 0.7840 (mmm) cc_final: 0.7605 (mmm) REVERT: J 515 SER cc_start: 0.7276 (OUTLIER) cc_final: 0.7057 (p) REVERT: J 641 GLU cc_start: 0.7630 (pt0) cc_final: 0.7315 (pt0) REVERT: J 679 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7754 (mttm) REVERT: K 903 MET cc_start: 0.7739 (mtp) cc_final: 0.7510 (mtp) REVERT: K 1074 CYS cc_start: 0.5978 (m) cc_final: 0.5666 (m) REVERT: K 1253 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.5329 (mtt180) REVERT: M 115 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.6989 (mm) REVERT: M 188 LYS cc_start: 0.8865 (ttmm) cc_final: 0.8541 (ttmm) REVERT: M 195 TRP cc_start: 0.8566 (t60) cc_final: 0.8117 (t60) REVERT: M 197 HIS cc_start: 0.8107 (m170) cc_final: 0.7604 (m170) REVERT: N 376 ASP cc_start: 0.8048 (t0) cc_final: 0.7723 (t0) REVERT: N 401 ARG cc_start: 0.8149 (ptt90) cc_final: 0.7712 (ptt90) REVERT: N 510 ASP cc_start: 0.8624 (t0) cc_final: 0.8345 (t0) REVERT: N 529 LYS cc_start: 0.7993 (tptp) cc_final: 0.7546 (tptp) REVERT: N 557 GLN cc_start: 0.7611 (mt0) cc_final: 0.7014 (tt0) REVERT: N 653 VAL cc_start: 0.8882 (OUTLIER) cc_final: 0.8496 (m) REVERT: N 690 TYR cc_start: 0.8614 (t80) cc_final: 0.8339 (t80) REVERT: O 920 GLU cc_start: 0.7641 (pm20) cc_final: 0.7378 (pm20) REVERT: O 1199 LYS cc_start: 0.8205 (mmmt) cc_final: 0.7847 (mmmt) outliers start: 183 outliers final: 132 residues processed: 1099 average time/residue: 0.4545 time to fit residues: 782.2473 Evaluate side-chains 1129 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 990 time to evaluate : 3.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1040 SER Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain C residue 1153 THR Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 569 GLN Chi-restraints excluded: chain F residue 583 ARG Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 658 MET Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 691 TYR Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 713 SER Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 1002 GLN Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1059 LEU Chi-restraints excluded: chain G residue 1114 LEU Chi-restraints excluded: chain G residue 1116 CYS Chi-restraints excluded: chain G residue 1132 THR Chi-restraints excluded: chain G residue 1136 LYS Chi-restraints excluded: chain G residue 1144 SER Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1241 LEU Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 251 TRP Chi-restraints excluded: chain J residue 361 CYS Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 420 THR Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 498 GLU Chi-restraints excluded: chain J residue 508 THR Chi-restraints excluded: chain J residue 515 SER Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 551 ASN Chi-restraints excluded: chain J residue 572 SER Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 653 VAL Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 ILE Chi-restraints excluded: chain J residue 718 CYS Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain J residue 744 LEU Chi-restraints excluded: chain K residue 822 MET Chi-restraints excluded: chain K residue 960 ASP Chi-restraints excluded: chain K residue 961 VAL Chi-restraints excluded: chain K residue 1040 SER Chi-restraints excluded: chain K residue 1046 VAL Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1097 LEU Chi-restraints excluded: chain K residue 1117 THR Chi-restraints excluded: chain K residue 1241 LEU Chi-restraints excluded: chain K residue 1253 ARG Chi-restraints excluded: chain M residue 115 ILE Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 469 VAL Chi-restraints excluded: chain N residue 475 THR Chi-restraints excluded: chain N residue 492 THR Chi-restraints excluded: chain N residue 496 THR Chi-restraints excluded: chain N residue 525 VAL Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 560 VAL Chi-restraints excluded: chain N residue 588 HIS Chi-restraints excluded: chain N residue 623 HIS Chi-restraints excluded: chain N residue 653 VAL Chi-restraints excluded: chain N residue 677 GLU Chi-restraints excluded: chain N residue 718 CYS Chi-restraints excluded: chain N residue 743 THR Chi-restraints excluded: chain O residue 923 VAL Chi-restraints excluded: chain O residue 964 ASN Chi-restraints excluded: chain O residue 996 LYS Chi-restraints excluded: chain O residue 1024 GLU Chi-restraints excluded: chain O residue 1075 GLN Chi-restraints excluded: chain O residue 1105 ILE Chi-restraints excluded: chain O residue 1107 GLU Chi-restraints excluded: chain O residue 1115 THR Chi-restraints excluded: chain O residue 1151 VAL Chi-restraints excluded: chain O residue 1156 GLU Chi-restraints excluded: chain O residue 1185 CYS Chi-restraints excluded: chain O residue 1244 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 4 optimal weight: 1.9990 chunk 357 optimal weight: 5.9990 chunk 355 optimal weight: 0.7980 chunk 320 optimal weight: 5.9990 chunk 324 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 122 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 184 optimal weight: 7.9990 chunk 402 optimal weight: 10.0000 chunk 306 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN B 673 GLN C 964 ASN E 145 HIS ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 HIS ** F 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 569 GLN G1001 ASN G1146 HIS I 172 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 ASN J 340 ASN J 559 HIS K1019 GLN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1170 HIS N 686 GLN O 917 GLN O1019 GLN O1226 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099564 restraints weight = 54709.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102762 restraints weight = 23257.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104815 restraints weight = 12502.008| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 33668 Z= 0.171 Angle : 0.616 19.659 45900 Z= 0.306 Chirality : 0.046 0.599 5124 Planarity : 0.005 0.057 5888 Dihedral : 4.703 54.815 4966 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.18 % Favored : 95.80 % Rotamer: Outliers : 5.61 % Allowed : 29.44 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.19 (0.13), residues: 4188 helix: 2.97 (0.23), residues: 432 sheet: 0.43 (0.15), residues: 1228 loop : -1.02 (0.12), residues: 2528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 195 HIS 0.009 0.001 HIS J 559 PHE 0.021 0.002 PHE N 339 TYR 0.020 0.002 TYR B 402 ARG 0.010 0.001 ARG G 930 Details of bonding type rmsd link_NAG-ASN : bond 0.01678 ( 12) link_NAG-ASN : angle 6.49744 ( 36) link_BETA1-4 : bond 0.00380 ( 8) link_BETA1-4 : angle 1.32928 ( 24) hydrogen bonds : bond 0.03937 ( 1245) hydrogen bonds : angle 4.51481 ( 3279) SS BOND : bond 0.00391 ( 68) SS BOND : angle 1.43350 ( 136) covalent geometry : bond 0.00395 (33580) covalent geometry : angle 0.58394 (45704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 1044 time to evaluate : 3.516 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 135 LEU cc_start: 0.8376 (mp) cc_final: 0.8090 (mp) REVERT: A 149 VAL cc_start: 0.8616 (t) cc_final: 0.8373 (p) REVERT: B 490 GLN cc_start: 0.7666 (mm110) cc_final: 0.7373 (mm110) REVERT: B 502 MET cc_start: 0.7375 (mtp) cc_final: 0.7162 (mtp) REVERT: B 532 TYR cc_start: 0.7989 (p90) cc_final: 0.7517 (p90) REVERT: B 543 THR cc_start: 0.8060 (OUTLIER) cc_final: 0.7853 (m) REVERT: B 586 LYS cc_start: 0.8425 (mttm) cc_final: 0.7953 (mtpt) REVERT: B 594 ASP cc_start: 0.7149 (t0) cc_final: 0.6832 (t0) REVERT: B 690 TYR cc_start: 0.8595 (t80) cc_final: 0.7989 (t80) REVERT: C 894 LYS cc_start: 0.8230 (mmtm) cc_final: 0.7840 (mmmm) REVERT: C 904 TRP cc_start: 0.8743 (p-90) cc_final: 0.8488 (p-90) REVERT: C 930 ARG cc_start: 0.8499 (ttp-110) cc_final: 0.8241 (ttp80) REVERT: C 997 ASP cc_start: 0.7435 (p0) cc_final: 0.7184 (p0) REVERT: C 1150 ASN cc_start: 0.7825 (t0) cc_final: 0.7441 (t0) REVERT: C 1242 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7910 (p) REVERT: E 186 HIS cc_start: 0.8624 (OUTLIER) cc_final: 0.7491 (p-80) REVERT: F 404 ASP cc_start: 0.8138 (t0) cc_final: 0.7937 (t0) REVERT: F 408 ILE cc_start: 0.8385 (mp) cc_final: 0.8110 (mm) REVERT: F 430 MET cc_start: 0.7421 (tmm) cc_final: 0.6782 (tmm) REVERT: F 490 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7382 (mm-40) REVERT: F 499 GLU cc_start: 0.7601 (pm20) cc_final: 0.7321 (pm20) REVERT: F 594 ASP cc_start: 0.7443 (t0) cc_final: 0.7085 (t0) REVERT: F 638 TYR cc_start: 0.8529 (p90) cc_final: 0.8215 (p90) REVERT: F 651 ILE cc_start: 0.8445 (mm) cc_final: 0.8176 (mt) REVERT: F 679 LYS cc_start: 0.8284 (mmmt) cc_final: 0.7921 (mmmt) REVERT: F 704 VAL cc_start: 0.8363 (t) cc_final: 0.8023 (p) REVERT: G 903 MET cc_start: 0.7821 (ttm) cc_final: 0.7347 (mtp) REVERT: G 1029 TYR cc_start: 0.8044 (t80) cc_final: 0.7773 (t80) REVERT: G 1120 THR cc_start: 0.8174 (m) cc_final: 0.7769 (p) REVERT: G 1122 THR cc_start: 0.8586 (p) cc_final: 0.8359 (p) REVERT: I 142 LYS cc_start: 0.8442 (tmmt) cc_final: 0.7679 (tmmt) REVERT: J 378 MET cc_start: 0.7825 (mmm) cc_final: 0.7046 (mmm) REVERT: J 490 GLN cc_start: 0.7597 (tp-100) cc_final: 0.7259 (tp-100) REVERT: J 502 MET cc_start: 0.8015 (mmm) cc_final: 0.7529 (mmm) REVERT: J 641 GLU cc_start: 0.7704 (pt0) cc_final: 0.7408 (pt0) REVERT: J 679 LYS cc_start: 0.8141 (mmtm) cc_final: 0.7792 (mttm) REVERT: K 903 MET cc_start: 0.7748 (mtp) cc_final: 0.7540 (mtp) REVERT: K 1074 CYS cc_start: 0.6012 (m) cc_final: 0.5608 (m) REVERT: M 113 MET cc_start: 0.5625 (mmm) cc_final: 0.5318 (mmm) REVERT: N 376 ASP cc_start: 0.8082 (t0) cc_final: 0.7793 (t0) REVERT: N 459 ARG cc_start: 0.8160 (ttm-80) cc_final: 0.7952 (ttm-80) REVERT: N 510 ASP cc_start: 0.8617 (t0) cc_final: 0.8391 (t0) REVERT: N 529 LYS cc_start: 0.8035 (tptp) cc_final: 0.7545 (tptp) REVERT: N 586 LYS cc_start: 0.8405 (ttmm) cc_final: 0.8139 (mmmm) REVERT: N 653 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8590 (m) REVERT: O 920 GLU cc_start: 0.7644 (pm20) cc_final: 0.7390 (pm20) REVERT: O 1035 LYS cc_start: 0.8208 (mtpp) cc_final: 0.7962 (ttmm) REVERT: O 1084 MET cc_start: 0.8055 (mmm) cc_final: 0.7846 (mtm) REVERT: O 1096 ASN cc_start: 0.8548 (t0) cc_final: 0.8251 (t0) REVERT: O 1199 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7917 (mmmt) outliers start: 201 outliers final: 163 residues processed: 1140 average time/residue: 0.4531 time to fit residues: 811.1854 Evaluate side-chains 1181 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1014 time to evaluate : 3.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 1003 ASP Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1040 SER Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1106 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1153 THR Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 195 TRP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 543 THR Chi-restraints excluded: chain F residue 583 ARG Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 711 LEU Chi-restraints excluded: chain F residue 713 SER Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 748 CYS Chi-restraints excluded: chain G residue 817 GLU Chi-restraints excluded: chain G residue 862 ILE Chi-restraints excluded: chain G residue 870 VAL Chi-restraints excluded: chain G residue 1002 GLN Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1059 LEU Chi-restraints excluded: chain G residue 1114 LEU Chi-restraints excluded: chain G residue 1116 CYS Chi-restraints excluded: chain G residue 1132 THR Chi-restraints excluded: chain G residue 1144 SER Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1214 PHE Chi-restraints excluded: chain G residue 1241 LEU Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 251 TRP Chi-restraints excluded: chain J residue 361 CYS Chi-restraints excluded: chain J residue 383 PHE Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 400 ILE Chi-restraints excluded: chain J residue 420 THR Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 508 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 551 ASN Chi-restraints excluded: chain J residue 567 LYS Chi-restraints excluded: chain J residue 572 SER Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 653 VAL Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 ILE Chi-restraints excluded: chain J residue 718 CYS Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain J residue 744 LEU Chi-restraints excluded: chain K residue 821 VAL Chi-restraints excluded: chain K residue 822 MET Chi-restraints excluded: chain K residue 844 LEU Chi-restraints excluded: chain K residue 960 ASP Chi-restraints excluded: chain K residue 961 VAL Chi-restraints excluded: chain K residue 1040 SER Chi-restraints excluded: chain K residue 1046 VAL Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1097 LEU Chi-restraints excluded: chain K residue 1117 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1241 LEU Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain N residue 394 ASN Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 469 VAL Chi-restraints excluded: chain N residue 475 THR Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 492 THR Chi-restraints excluded: chain N residue 496 THR Chi-restraints excluded: chain N residue 525 VAL Chi-restraints excluded: chain N residue 531 LYS Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 552 THR Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain N residue 623 HIS Chi-restraints excluded: chain N residue 653 VAL Chi-restraints excluded: chain N residue 677 GLU Chi-restraints excluded: chain N residue 708 LEU Chi-restraints excluded: chain N residue 712 ILE Chi-restraints excluded: chain N residue 718 CYS Chi-restraints excluded: chain N residue 722 VAL Chi-restraints excluded: chain N residue 743 THR Chi-restraints excluded: chain O residue 862 ILE Chi-restraints excluded: chain O residue 923 VAL Chi-restraints excluded: chain O residue 951 MET Chi-restraints excluded: chain O residue 996 LYS Chi-restraints excluded: chain O residue 1024 GLU Chi-restraints excluded: chain O residue 1075 GLN Chi-restraints excluded: chain O residue 1105 ILE Chi-restraints excluded: chain O residue 1107 GLU Chi-restraints excluded: chain O residue 1115 THR Chi-restraints excluded: chain O residue 1116 CYS Chi-restraints excluded: chain O residue 1132 THR Chi-restraints excluded: chain O residue 1151 VAL Chi-restraints excluded: chain O residue 1156 GLU Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1185 CYS Chi-restraints excluded: chain O residue 1226 GLN Chi-restraints excluded: chain O residue 1244 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 250 optimal weight: 4.9990 chunk 338 optimal weight: 0.8980 chunk 408 optimal weight: 20.0000 chunk 403 optimal weight: 40.0000 chunk 331 optimal weight: 3.9990 chunk 314 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 chunk 221 optimal weight: 2.9990 chunk 256 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 234 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN A 252 ASN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 GLN B 665 ASN C1146 HIS ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1155 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 623 HIS J 673 GLN K1019 GLN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 686 GLN O 917 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.098198 restraints weight = 54729.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101380 restraints weight = 23356.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103410 restraints weight = 12643.434| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 33668 Z= 0.229 Angle : 0.658 19.310 45900 Z= 0.330 Chirality : 0.047 0.641 5124 Planarity : 0.005 0.091 5888 Dihedral : 4.915 57.769 4966 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.61 % Favored : 95.37 % Rotamer: Outliers : 6.40 % Allowed : 29.39 % Favored : 64.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.30 (0.13), residues: 4188 helix: 2.80 (0.24), residues: 432 sheet: 0.27 (0.15), residues: 1208 loop : -1.01 (0.12), residues: 2548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 195 HIS 0.010 0.001 HIS J 559 PHE 0.022 0.002 PHE N 715 TYR 0.022 0.002 TYR B 402 ARG 0.011 0.001 ARG G 930 Details of bonding type rmsd link_NAG-ASN : bond 0.01424 ( 12) link_NAG-ASN : angle 6.64669 ( 36) link_BETA1-4 : bond 0.00457 ( 8) link_BETA1-4 : angle 1.35566 ( 24) hydrogen bonds : bond 0.04424 ( 1245) hydrogen bonds : angle 4.64321 ( 3279) SS BOND : bond 0.00539 ( 68) SS BOND : angle 1.65371 ( 136) covalent geometry : bond 0.00527 (33580) covalent geometry : angle 0.62563 (45704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 229 poor density : 1025 time to evaluate : 3.419 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: A 135 LEU cc_start: 0.8431 (mp) cc_final: 0.8217 (mt) REVERT: A 149 VAL cc_start: 0.8726 (t) cc_final: 0.8484 (p) REVERT: B 354 ASP cc_start: 0.7365 (OUTLIER) cc_final: 0.6997 (t70) REVERT: B 384 SER cc_start: 0.8225 (m) cc_final: 0.7790 (p) REVERT: B 396 ASP cc_start: 0.8179 (t0) cc_final: 0.7947 (t0) REVERT: B 490 GLN cc_start: 0.7710 (mm110) cc_final: 0.7394 (mm110) REVERT: B 502 MET cc_start: 0.7421 (mtp) cc_final: 0.7199 (mtp) REVERT: B 532 TYR cc_start: 0.8001 (p90) cc_final: 0.7578 (p90) REVERT: B 586 LYS cc_start: 0.8446 (mttm) cc_final: 0.7930 (mtpt) REVERT: B 594 ASP cc_start: 0.7191 (t0) cc_final: 0.6868 (t0) REVERT: B 690 TYR cc_start: 0.8492 (t80) cc_final: 0.7912 (t80) REVERT: C 894 LYS cc_start: 0.8255 (mmtm) cc_final: 0.7872 (mmmm) REVERT: C 904 TRP cc_start: 0.8755 (p-90) cc_final: 0.8551 (p-90) REVERT: C 997 ASP cc_start: 0.7400 (p0) cc_final: 0.7113 (p0) REVERT: C 1028 LEU cc_start: 0.8557 (tp) cc_final: 0.8349 (tt) REVERT: C 1122 THR cc_start: 0.8613 (m) cc_final: 0.8277 (p) REVERT: C 1135 TYR cc_start: 0.8237 (p90) cc_final: 0.7543 (p90) REVERT: C 1150 ASN cc_start: 0.7842 (t0) cc_final: 0.7616 (t0) REVERT: E 186 HIS cc_start: 0.8592 (OUTLIER) cc_final: 0.7174 (p-80) REVERT: E 188 LYS cc_start: 0.6311 (mmtt) cc_final: 0.5641 (mmtt) REVERT: F 404 ASP cc_start: 0.8177 (t0) cc_final: 0.7953 (t0) REVERT: F 408 ILE cc_start: 0.8366 (mp) cc_final: 0.8090 (mm) REVERT: F 430 MET cc_start: 0.7461 (tmm) cc_final: 0.7044 (tmm) REVERT: F 489 TYR cc_start: 0.8344 (m-80) cc_final: 0.7645 (m-80) REVERT: F 499 GLU cc_start: 0.7617 (pm20) cc_final: 0.7369 (pm20) REVERT: F 502 MET cc_start: 0.7719 (mmt) cc_final: 0.7493 (mmm) REVERT: F 638 TYR cc_start: 0.8547 (p90) cc_final: 0.8236 (p90) REVERT: F 651 ILE cc_start: 0.8491 (mm) cc_final: 0.8231 (mt) REVERT: F 679 LYS cc_start: 0.8318 (mmmt) cc_final: 0.7952 (mmmt) REVERT: F 704 VAL cc_start: 0.8380 (t) cc_final: 0.8037 (p) REVERT: G 1029 TYR cc_start: 0.8033 (t80) cc_final: 0.7773 (t80) REVERT: G 1120 THR cc_start: 0.8285 (m) cc_final: 0.7891 (p) REVERT: G 1122 THR cc_start: 0.8630 (p) cc_final: 0.8404 (p) REVERT: I 142 LYS cc_start: 0.8456 (tmmt) cc_final: 0.7711 (tmmt) REVERT: I 180 ASP cc_start: 0.7993 (p0) cc_final: 0.7528 (p0) REVERT: J 378 MET cc_start: 0.7813 (mmm) cc_final: 0.7497 (tpp) REVERT: J 399 LYS cc_start: 0.8485 (mtpp) cc_final: 0.7665 (mtmm) REVERT: J 490 GLN cc_start: 0.7642 (tp-100) cc_final: 0.7278 (tp-100) REVERT: J 502 MET cc_start: 0.8072 (mmm) cc_final: 0.7527 (mmm) REVERT: J 569 GLN cc_start: 0.7273 (tp-100) cc_final: 0.6768 (tt0) REVERT: J 641 GLU cc_start: 0.7697 (pt0) cc_final: 0.7399 (pt0) REVERT: J 679 LYS cc_start: 0.8149 (mmtm) cc_final: 0.7774 (mttm) REVERT: M 113 MET cc_start: 0.5675 (mmm) cc_final: 0.5312 (mmm) REVERT: M 195 TRP cc_start: 0.8636 (t60) cc_final: 0.8218 (t60) REVERT: N 376 ASP cc_start: 0.8097 (t0) cc_final: 0.7817 (t0) REVERT: N 399 LYS cc_start: 0.8063 (mtpp) cc_final: 0.7852 (mtpp) REVERT: N 410 ASN cc_start: 0.7907 (m-40) cc_final: 0.7633 (m-40) REVERT: N 459 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7539 (ptm160) REVERT: N 510 ASP cc_start: 0.8619 (t0) cc_final: 0.8367 (t0) REVERT: N 516 GLN cc_start: 0.8741 (mm110) cc_final: 0.8500 (mm-40) REVERT: N 529 LYS cc_start: 0.8147 (tptp) cc_final: 0.7688 (tptp) REVERT: N 623 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7513 (p-80) REVERT: N 653 VAL cc_start: 0.8982 (OUTLIER) cc_final: 0.8618 (m) REVERT: N 727 LYS cc_start: 0.8807 (ttmt) cc_final: 0.8576 (ttmm) REVERT: O 920 GLU cc_start: 0.7651 (pm20) cc_final: 0.7330 (pm20) REVERT: O 959 VAL cc_start: 0.8442 (p) cc_final: 0.8116 (m) REVERT: O 1079 ASN cc_start: 0.8331 (t0) cc_final: 0.8031 (t0) REVERT: O 1096 ASN cc_start: 0.8559 (t0) cc_final: 0.8256 (t0) REVERT: O 1150 ASN cc_start: 0.8422 (t0) cc_final: 0.8131 (t0) REVERT: O 1199 LYS cc_start: 0.8253 (mmmt) cc_final: 0.7887 (mmmt) outliers start: 229 outliers final: 178 residues processed: 1145 average time/residue: 0.4259 time to fit residues: 773.5869 Evaluate side-chains 1196 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 1014 time to evaluate : 3.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 145 HIS Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 1003 ASP Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1040 SER Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1153 THR Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 195 TRP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 540 ASN Chi-restraints excluded: chain F residue 543 THR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 583 ARG Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 658 MET Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 713 SER Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 748 CYS Chi-restraints excluded: chain G residue 862 ILE Chi-restraints excluded: chain G residue 1002 GLN Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1059 LEU Chi-restraints excluded: chain G residue 1075 GLN Chi-restraints excluded: chain G residue 1114 LEU Chi-restraints excluded: chain G residue 1116 CYS Chi-restraints excluded: chain G residue 1132 THR Chi-restraints excluded: chain G residue 1144 SER Chi-restraints excluded: chain G residue 1153 THR Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1158 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1241 LEU Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 173 ILE Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 186 HIS Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 251 TRP Chi-restraints excluded: chain J residue 361 CYS Chi-restraints excluded: chain J residue 383 PHE Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 400 ILE Chi-restraints excluded: chain J residue 420 THR Chi-restraints excluded: chain J residue 467 GLN Chi-restraints excluded: chain J residue 472 GLU Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 508 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 551 ASN Chi-restraints excluded: chain J residue 559 HIS Chi-restraints excluded: chain J residue 561 SER Chi-restraints excluded: chain J residue 567 LYS Chi-restraints excluded: chain J residue 572 SER Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 653 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 ILE Chi-restraints excluded: chain J residue 718 CYS Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain J residue 744 LEU Chi-restraints excluded: chain K residue 822 MET Chi-restraints excluded: chain K residue 844 LEU Chi-restraints excluded: chain K residue 960 ASP Chi-restraints excluded: chain K residue 1040 SER Chi-restraints excluded: chain K residue 1046 VAL Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1095 MET Chi-restraints excluded: chain K residue 1097 LEU Chi-restraints excluded: chain K residue 1117 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1196 GLU Chi-restraints excluded: chain K residue 1241 LEU Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 215 LYS Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain N residue 394 ASN Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 418 VAL Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 469 VAL Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 492 THR Chi-restraints excluded: chain N residue 496 THR Chi-restraints excluded: chain N residue 525 VAL Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 552 THR Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain N residue 623 HIS Chi-restraints excluded: chain N residue 653 VAL Chi-restraints excluded: chain N residue 664 ASN Chi-restraints excluded: chain N residue 677 GLU Chi-restraints excluded: chain N residue 712 ILE Chi-restraints excluded: chain N residue 718 CYS Chi-restraints excluded: chain N residue 722 VAL Chi-restraints excluded: chain N residue 735 THR Chi-restraints excluded: chain N residue 743 THR Chi-restraints excluded: chain O residue 862 ILE Chi-restraints excluded: chain O residue 923 VAL Chi-restraints excluded: chain O residue 951 MET Chi-restraints excluded: chain O residue 996 LYS Chi-restraints excluded: chain O residue 1024 GLU Chi-restraints excluded: chain O residue 1075 GLN Chi-restraints excluded: chain O residue 1105 ILE Chi-restraints excluded: chain O residue 1107 GLU Chi-restraints excluded: chain O residue 1110 THR Chi-restraints excluded: chain O residue 1115 THR Chi-restraints excluded: chain O residue 1116 CYS Chi-restraints excluded: chain O residue 1132 THR Chi-restraints excluded: chain O residue 1151 VAL Chi-restraints excluded: chain O residue 1156 GLU Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1185 CYS Chi-restraints excluded: chain O residue 1244 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 315 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 246 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 275 optimal weight: 0.8980 chunk 344 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 201 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 623 HIS K 845 GLN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 386 GLN N 517 GLN N 557 GLN N 686 GLN O 917 GLN O 964 ASN O1045 HIS O1226 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.117710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.099343 restraints weight = 54567.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.102571 restraints weight = 23071.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.104636 restraints weight = 12384.079| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 33668 Z= 0.155 Angle : 0.644 19.361 45900 Z= 0.320 Chirality : 0.046 0.611 5124 Planarity : 0.005 0.055 5888 Dihedral : 4.791 54.656 4966 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 5.87 % Allowed : 30.61 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.26 (0.13), residues: 4188 helix: 2.88 (0.23), residues: 432 sheet: 0.38 (0.15), residues: 1264 loop : -1.07 (0.12), residues: 2492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP E 195 HIS 0.013 0.001 HIS N 395 PHE 0.022 0.001 PHE N 339 TYR 0.019 0.002 TYR B 402 ARG 0.012 0.001 ARG G 930 Details of bonding type rmsd link_NAG-ASN : bond 0.01494 ( 12) link_NAG-ASN : angle 6.48937 ( 36) link_BETA1-4 : bond 0.00415 ( 8) link_BETA1-4 : angle 1.42243 ( 24) hydrogen bonds : bond 0.04011 ( 1245) hydrogen bonds : angle 4.58275 ( 3279) SS BOND : bond 0.00352 ( 68) SS BOND : angle 1.68915 ( 136) covalent geometry : bond 0.00360 (33580) covalent geometry : angle 0.61114 (45704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1242 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 1032 time to evaluate : 3.534 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 135 LEU cc_start: 0.8392 (mp) cc_final: 0.8174 (mt) REVERT: A 149 VAL cc_start: 0.8798 (t) cc_final: 0.8556 (p) REVERT: B 490 GLN cc_start: 0.7690 (mm110) cc_final: 0.7379 (mm110) REVERT: B 502 MET cc_start: 0.7347 (mtp) cc_final: 0.7145 (mtp) REVERT: B 532 TYR cc_start: 0.7958 (p90) cc_final: 0.7475 (p90) REVERT: B 586 LYS cc_start: 0.8446 (mttm) cc_final: 0.7948 (mtpt) REVERT: B 594 ASP cc_start: 0.7254 (t0) cc_final: 0.6867 (t0) REVERT: B 658 MET cc_start: 0.7515 (tmm) cc_final: 0.7282 (ttp) REVERT: B 690 TYR cc_start: 0.8580 (t80) cc_final: 0.8064 (t80) REVERT: C 894 LYS cc_start: 0.8216 (mmtm) cc_final: 0.7834 (mmmm) REVERT: C 904 TRP cc_start: 0.8724 (p-90) cc_final: 0.8487 (p-90) REVERT: C 997 ASP cc_start: 0.7408 (p0) cc_final: 0.7119 (p0) REVERT: C 1028 LEU cc_start: 0.8592 (tp) cc_final: 0.8359 (tt) REVERT: C 1135 TYR cc_start: 0.8213 (p90) cc_final: 0.7537 (p90) REVERT: C 1150 ASN cc_start: 0.7806 (t0) cc_final: 0.7570 (t0) REVERT: E 186 HIS cc_start: 0.8609 (OUTLIER) cc_final: 0.7499 (p-80) REVERT: F 404 ASP cc_start: 0.8132 (t0) cc_final: 0.7914 (t0) REVERT: F 408 ILE cc_start: 0.8354 (mp) cc_final: 0.8093 (mm) REVERT: F 430 MET cc_start: 0.7466 (tmm) cc_final: 0.7063 (tmm) REVERT: F 489 TYR cc_start: 0.8341 (m-80) cc_final: 0.7551 (m-80) REVERT: F 490 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7346 (mm-40) REVERT: F 499 GLU cc_start: 0.7624 (pm20) cc_final: 0.7374 (pm20) REVERT: F 638 TYR cc_start: 0.8552 (p90) cc_final: 0.8238 (p90) REVERT: F 651 ILE cc_start: 0.8467 (mm) cc_final: 0.8187 (mt) REVERT: F 679 LYS cc_start: 0.8332 (mmmt) cc_final: 0.7956 (mmmt) REVERT: G 964 ASN cc_start: 0.8306 (p0) cc_final: 0.7857 (p0) REVERT: G 1029 TYR cc_start: 0.8025 (t80) cc_final: 0.7722 (t80) REVERT: G 1120 THR cc_start: 0.8274 (m) cc_final: 0.7901 (p) REVERT: G 1122 THR cc_start: 0.8667 (p) cc_final: 0.8455 (p) REVERT: I 142 LYS cc_start: 0.8448 (tmmt) cc_final: 0.7790 (tmmt) REVERT: I 180 ASP cc_start: 0.8027 (p0) cc_final: 0.7553 (p0) REVERT: I 195 TRP cc_start: 0.7320 (t60) cc_final: 0.6955 (t60) REVERT: J 371 ARG cc_start: 0.7923 (mtt90) cc_final: 0.7716 (mtt-85) REVERT: J 378 MET cc_start: 0.7795 (mmm) cc_final: 0.7525 (tpp) REVERT: J 399 LYS cc_start: 0.8501 (mtpp) cc_final: 0.7655 (mtmm) REVERT: J 490 GLN cc_start: 0.7670 (tp-100) cc_final: 0.7292 (tp-100) REVERT: J 502 MET cc_start: 0.8067 (mmm) cc_final: 0.7515 (mmm) REVERT: J 569 GLN cc_start: 0.7234 (tp-100) cc_final: 0.6721 (tt0) REVERT: J 641 GLU cc_start: 0.7715 (pt0) cc_final: 0.7420 (pt0) REVERT: J 679 LYS cc_start: 0.8150 (mmtm) cc_final: 0.7762 (mttm) REVERT: K 917 GLN cc_start: 0.8178 (tt0) cc_final: 0.7962 (tt0) REVERT: K 1031 ASN cc_start: 0.8697 (t0) cc_final: 0.8306 (t0) REVERT: K 1249 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.7800 (mm) REVERT: M 113 MET cc_start: 0.5695 (mmm) cc_final: 0.5318 (mmm) REVERT: M 195 TRP cc_start: 0.8597 (t60) cc_final: 0.8107 (t60) REVERT: N 376 ASP cc_start: 0.8086 (t0) cc_final: 0.7802 (t0) REVERT: N 401 ARG cc_start: 0.8343 (ptt180) cc_final: 0.8070 (ptt90) REVERT: N 459 ARG cc_start: 0.8086 (ttm-80) cc_final: 0.7520 (ptm160) REVERT: N 510 ASP cc_start: 0.8594 (t0) cc_final: 0.8352 (t0) REVERT: N 529 LYS cc_start: 0.8161 (tptp) cc_final: 0.7648 (tptp) REVERT: N 534 CYS cc_start: 0.6327 (m) cc_final: 0.5972 (m) REVERT: N 653 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8603 (m) REVERT: N 717 SER cc_start: 0.8193 (t) cc_final: 0.7957 (t) REVERT: N 727 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8573 (ttmm) REVERT: O 920 GLU cc_start: 0.7647 (pm20) cc_final: 0.7311 (pm20) REVERT: O 959 VAL cc_start: 0.8413 (p) cc_final: 0.8134 (m) REVERT: O 1096 ASN cc_start: 0.8517 (t0) cc_final: 0.8227 (t0) REVERT: O 1150 ASN cc_start: 0.8373 (t0) cc_final: 0.7962 (t0) REVERT: O 1199 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7894 (mmmt) REVERT: O 1210 SER cc_start: 0.7830 (p) cc_final: 0.7582 (p) outliers start: 210 outliers final: 178 residues processed: 1136 average time/residue: 0.4635 time to fit residues: 834.8043 Evaluate side-chains 1197 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 1016 time to evaluate : 3.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1040 SER Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1153 THR Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 195 TRP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 543 THR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 583 ARG Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 658 MET Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 713 SER Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 729 LEU Chi-restraints excluded: chain F residue 748 CYS Chi-restraints excluded: chain G residue 1032 THR Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1059 LEU Chi-restraints excluded: chain G residue 1114 LEU Chi-restraints excluded: chain G residue 1116 CYS Chi-restraints excluded: chain G residue 1132 THR Chi-restraints excluded: chain G residue 1144 SER Chi-restraints excluded: chain G residue 1153 THR Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1158 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1214 PHE Chi-restraints excluded: chain G residue 1241 LEU Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 186 HIS Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 251 TRP Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 420 THR Chi-restraints excluded: chain J residue 472 GLU Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 508 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 551 ASN Chi-restraints excluded: chain J residue 561 SER Chi-restraints excluded: chain J residue 567 LYS Chi-restraints excluded: chain J residue 572 SER Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 577 ARG Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 653 VAL Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 ILE Chi-restraints excluded: chain J residue 718 CYS Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain J residue 744 LEU Chi-restraints excluded: chain K residue 822 MET Chi-restraints excluded: chain K residue 844 LEU Chi-restraints excluded: chain K residue 960 ASP Chi-restraints excluded: chain K residue 1040 SER Chi-restraints excluded: chain K residue 1046 VAL Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1095 MET Chi-restraints excluded: chain K residue 1097 LEU Chi-restraints excluded: chain K residue 1100 SER Chi-restraints excluded: chain K residue 1117 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1196 GLU Chi-restraints excluded: chain K residue 1241 LEU Chi-restraints excluded: chain K residue 1249 ILE Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain N residue 394 ASN Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 469 VAL Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 492 THR Chi-restraints excluded: chain N residue 517 GLN Chi-restraints excluded: chain N residue 525 VAL Chi-restraints excluded: chain N residue 531 LYS Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 552 THR Chi-restraints excluded: chain N residue 560 VAL Chi-restraints excluded: chain N residue 569 GLN Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain N residue 648 GLU Chi-restraints excluded: chain N residue 653 VAL Chi-restraints excluded: chain N residue 677 GLU Chi-restraints excluded: chain N residue 718 CYS Chi-restraints excluded: chain N residue 743 THR Chi-restraints excluded: chain O residue 862 ILE Chi-restraints excluded: chain O residue 923 VAL Chi-restraints excluded: chain O residue 951 MET Chi-restraints excluded: chain O residue 964 ASN Chi-restraints excluded: chain O residue 996 LYS Chi-restraints excluded: chain O residue 1024 GLU Chi-restraints excluded: chain O residue 1075 GLN Chi-restraints excluded: chain O residue 1105 ILE Chi-restraints excluded: chain O residue 1107 GLU Chi-restraints excluded: chain O residue 1115 THR Chi-restraints excluded: chain O residue 1116 CYS Chi-restraints excluded: chain O residue 1132 THR Chi-restraints excluded: chain O residue 1151 VAL Chi-restraints excluded: chain O residue 1156 GLU Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1185 CYS Chi-restraints excluded: chain O residue 1213 VAL Chi-restraints excluded: chain O residue 1244 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 387 optimal weight: 20.0000 chunk 241 optimal weight: 2.9990 chunk 104 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 278 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 154 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 226 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN C 964 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1079 ASN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 623 HIS K 845 GLN K1019 GLN K1067 ASN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 517 GLN N 686 GLN O 917 GLN ** O 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1226 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098014 restraints weight = 54609.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101194 restraints weight = 23256.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103226 restraints weight = 12591.793| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 33668 Z= 0.197 Angle : 0.665 19.938 45900 Z= 0.331 Chirality : 0.047 0.609 5124 Planarity : 0.005 0.054 5888 Dihedral : 4.799 41.239 4964 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.80 % Favored : 95.18 % Rotamer: Outliers : 6.03 % Allowed : 30.67 % Favored : 63.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.35 (0.13), residues: 4188 helix: 2.84 (0.24), residues: 432 sheet: 0.27 (0.15), residues: 1260 loop : -1.10 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 195 HIS 0.008 0.001 HIS J 559 PHE 0.022 0.002 PHE N 715 TYR 0.022 0.002 TYR B 402 ARG 0.007 0.001 ARG C1014 Details of bonding type rmsd link_NAG-ASN : bond 0.01519 ( 12) link_NAG-ASN : angle 6.59878 ( 36) link_BETA1-4 : bond 0.00413 ( 8) link_BETA1-4 : angle 1.42082 ( 24) hydrogen bonds : bond 0.04243 ( 1245) hydrogen bonds : angle 4.61559 ( 3279) SS BOND : bond 0.00360 ( 68) SS BOND : angle 1.77097 ( 136) covalent geometry : bond 0.00456 (33580) covalent geometry : angle 0.63158 (45704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1042 time to evaluate : 3.482 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: symmetry clash REVERT: A 135 LEU cc_start: 0.8397 (mp) cc_final: 0.8177 (mt) REVERT: A 149 VAL cc_start: 0.8839 (t) cc_final: 0.8624 (p) REVERT: A 177 MET cc_start: 0.8116 (ptp) cc_final: 0.7911 (ptp) REVERT: B 354 ASP cc_start: 0.7348 (OUTLIER) cc_final: 0.6980 (t70) REVERT: B 384 SER cc_start: 0.8226 (m) cc_final: 0.7787 (p) REVERT: B 490 GLN cc_start: 0.7727 (mm110) cc_final: 0.7389 (mm110) REVERT: B 502 MET cc_start: 0.7365 (mtp) cc_final: 0.7146 (mtp) REVERT: B 504 MET cc_start: 0.7980 (ttm) cc_final: 0.7717 (ttt) REVERT: B 529 LYS cc_start: 0.8225 (ttmm) cc_final: 0.7882 (ptmm) REVERT: B 544 THR cc_start: 0.7589 (t) cc_final: 0.7278 (m) REVERT: B 586 LYS cc_start: 0.8417 (mttm) cc_final: 0.7936 (mtpt) REVERT: B 594 ASP cc_start: 0.7228 (t0) cc_final: 0.6866 (t0) REVERT: B 604 ARG cc_start: 0.7917 (ttm-80) cc_final: 0.7642 (ptp-110) REVERT: B 658 MET cc_start: 0.7518 (tmm) cc_final: 0.7302 (ttp) REVERT: B 690 TYR cc_start: 0.8476 (t80) cc_final: 0.7888 (t80) REVERT: C 894 LYS cc_start: 0.8245 (mmtm) cc_final: 0.7851 (mmmm) REVERT: C 904 TRP cc_start: 0.8743 (p-90) cc_final: 0.8514 (p-90) REVERT: C 997 ASP cc_start: 0.7405 (p0) cc_final: 0.7144 (p0) REVERT: C 1023 VAL cc_start: 0.8313 (OUTLIER) cc_final: 0.8105 (p) REVERT: C 1028 LEU cc_start: 0.8573 (tp) cc_final: 0.8328 (tt) REVERT: C 1150 ASN cc_start: 0.7800 (t0) cc_final: 0.7567 (t0) REVERT: E 186 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.7469 (p-80) REVERT: F 404 ASP cc_start: 0.8163 (t0) cc_final: 0.7932 (t0) REVERT: F 408 ILE cc_start: 0.8342 (mp) cc_final: 0.8091 (mm) REVERT: F 430 MET cc_start: 0.7487 (tmm) cc_final: 0.7105 (tmm) REVERT: F 490 GLN cc_start: 0.7616 (mm-40) cc_final: 0.7410 (mm-40) REVERT: F 499 GLU cc_start: 0.7625 (pm20) cc_final: 0.7375 (pm20) REVERT: F 638 TYR cc_start: 0.8524 (p90) cc_final: 0.8210 (p90) REVERT: F 679 LYS cc_start: 0.8314 (mmmt) cc_final: 0.7970 (mmmt) REVERT: G 894 LYS cc_start: 0.8001 (mmtp) cc_final: 0.7795 (mmtp) REVERT: G 964 ASN cc_start: 0.8274 (p0) cc_final: 0.7876 (p0) REVERT: G 1029 TYR cc_start: 0.8036 (t80) cc_final: 0.7718 (t80) REVERT: G 1115 THR cc_start: 0.8519 (t) cc_final: 0.8314 (p) REVERT: G 1120 THR cc_start: 0.8306 (m) cc_final: 0.7933 (p) REVERT: G 1122 THR cc_start: 0.8683 (p) cc_final: 0.8473 (p) REVERT: I 142 LYS cc_start: 0.8453 (tmmt) cc_final: 0.7807 (tmmt) REVERT: I 195 TRP cc_start: 0.7332 (t60) cc_final: 0.7037 (t60) REVERT: J 371 ARG cc_start: 0.7937 (mtt90) cc_final: 0.7727 (mtt-85) REVERT: J 378 MET cc_start: 0.7829 (mmm) cc_final: 0.7535 (tpp) REVERT: J 399 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8122 (mtmm) REVERT: J 490 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7362 (tp-100) REVERT: J 502 MET cc_start: 0.8082 (mmm) cc_final: 0.7630 (mmm) REVERT: J 569 GLN cc_start: 0.7276 (tp-100) cc_final: 0.6791 (tt0) REVERT: J 641 GLU cc_start: 0.7707 (pt0) cc_final: 0.7421 (pt0) REVERT: J 679 LYS cc_start: 0.8112 (mmtm) cc_final: 0.7751 (mttm) REVERT: K 917 GLN cc_start: 0.8164 (tt0) cc_final: 0.7958 (tt0) REVERT: K 1249 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7883 (mm) REVERT: M 113 MET cc_start: 0.5760 (mmm) cc_final: 0.5365 (mmm) REVERT: M 195 TRP cc_start: 0.8602 (t60) cc_final: 0.8127 (t60) REVERT: N 376 ASP cc_start: 0.8097 (t0) cc_final: 0.7805 (t0) REVERT: N 410 ASN cc_start: 0.7910 (m-40) cc_final: 0.7629 (m-40) REVERT: N 459 ARG cc_start: 0.8075 (ttm-80) cc_final: 0.7515 (ptm160) REVERT: N 510 ASP cc_start: 0.8601 (t0) cc_final: 0.8328 (t0) REVERT: N 534 CYS cc_start: 0.6336 (m) cc_final: 0.5959 (m) REVERT: N 547 ASP cc_start: 0.8224 (m-30) cc_final: 0.7503 (t0) REVERT: N 557 GLN cc_start: 0.8294 (mt0) cc_final: 0.7880 (mp10) REVERT: N 653 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8613 (m) REVERT: N 717 SER cc_start: 0.8219 (t) cc_final: 0.8012 (t) REVERT: N 727 LYS cc_start: 0.8796 (ttmt) cc_final: 0.8565 (ttmm) REVERT: O 920 GLU cc_start: 0.7643 (pm20) cc_final: 0.7318 (pm20) REVERT: O 959 VAL cc_start: 0.8428 (p) cc_final: 0.8156 (m) REVERT: O 1035 LYS cc_start: 0.8296 (ttpp) cc_final: 0.7907 (ttmm) REVERT: O 1079 ASN cc_start: 0.8330 (t0) cc_final: 0.8106 (t0) REVERT: O 1096 ASN cc_start: 0.8525 (t0) cc_final: 0.8226 (t0) REVERT: O 1150 ASN cc_start: 0.8339 (t0) cc_final: 0.7881 (t0) REVERT: O 1199 LYS cc_start: 0.8353 (mmmt) cc_final: 0.7960 (mmmt) REVERT: O 1210 SER cc_start: 0.7837 (p) cc_final: 0.7539 (p) outliers start: 216 outliers final: 191 residues processed: 1154 average time/residue: 0.4415 time to fit residues: 803.0598 Evaluate side-chains 1227 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 1031 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 555 ILE Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 637 GLN Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 722 VAL Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 910 PHE Chi-restraints excluded: chain C residue 1003 ASP Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1040 SER Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1153 THR Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 176 HIS Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 195 TRP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain F residue 543 THR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 583 ARG Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 658 MET Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 713 SER Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 729 LEU Chi-restraints excluded: chain F residue 748 CYS Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1059 LEU Chi-restraints excluded: chain G residue 1075 GLN Chi-restraints excluded: chain G residue 1114 LEU Chi-restraints excluded: chain G residue 1116 CYS Chi-restraints excluded: chain G residue 1144 SER Chi-restraints excluded: chain G residue 1153 THR Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1158 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1214 PHE Chi-restraints excluded: chain G residue 1241 LEU Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 186 HIS Chi-restraints excluded: chain I residue 190 GLU Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 231 VAL Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 251 TRP Chi-restraints excluded: chain J residue 383 PHE Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 420 THR Chi-restraints excluded: chain J residue 467 GLN Chi-restraints excluded: chain J residue 472 GLU Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 508 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 524 THR Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 551 ASN Chi-restraints excluded: chain J residue 559 HIS Chi-restraints excluded: chain J residue 561 SER Chi-restraints excluded: chain J residue 567 LYS Chi-restraints excluded: chain J residue 572 SER Chi-restraints excluded: chain J residue 575 VAL Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 625 THR Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 653 VAL Chi-restraints excluded: chain J residue 694 LEU Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 ILE Chi-restraints excluded: chain J residue 718 CYS Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain J residue 744 LEU Chi-restraints excluded: chain K residue 822 MET Chi-restraints excluded: chain K residue 835 GLU Chi-restraints excluded: chain K residue 844 LEU Chi-restraints excluded: chain K residue 960 ASP Chi-restraints excluded: chain K residue 1003 ASP Chi-restraints excluded: chain K residue 1019 GLN Chi-restraints excluded: chain K residue 1040 SER Chi-restraints excluded: chain K residue 1046 VAL Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1097 LEU Chi-restraints excluded: chain K residue 1100 SER Chi-restraints excluded: chain K residue 1117 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1185 CYS Chi-restraints excluded: chain K residue 1196 GLU Chi-restraints excluded: chain K residue 1241 LEU Chi-restraints excluded: chain K residue 1249 ILE Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain N residue 394 ASN Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 469 VAL Chi-restraints excluded: chain N residue 487 THR Chi-restraints excluded: chain N residue 492 THR Chi-restraints excluded: chain N residue 517 GLN Chi-restraints excluded: chain N residue 525 VAL Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 552 THR Chi-restraints excluded: chain N residue 569 GLN Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain N residue 623 HIS Chi-restraints excluded: chain N residue 648 GLU Chi-restraints excluded: chain N residue 653 VAL Chi-restraints excluded: chain N residue 677 GLU Chi-restraints excluded: chain N residue 712 ILE Chi-restraints excluded: chain N residue 718 CYS Chi-restraints excluded: chain N residue 735 THR Chi-restraints excluded: chain N residue 743 THR Chi-restraints excluded: chain O residue 862 ILE Chi-restraints excluded: chain O residue 923 VAL Chi-restraints excluded: chain O residue 951 MET Chi-restraints excluded: chain O residue 996 LYS Chi-restraints excluded: chain O residue 1024 GLU Chi-restraints excluded: chain O residue 1040 SER Chi-restraints excluded: chain O residue 1075 GLN Chi-restraints excluded: chain O residue 1105 ILE Chi-restraints excluded: chain O residue 1107 GLU Chi-restraints excluded: chain O residue 1110 THR Chi-restraints excluded: chain O residue 1115 THR Chi-restraints excluded: chain O residue 1116 CYS Chi-restraints excluded: chain O residue 1132 THR Chi-restraints excluded: chain O residue 1151 VAL Chi-restraints excluded: chain O residue 1156 GLU Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1185 CYS Chi-restraints excluded: chain O residue 1213 VAL Chi-restraints excluded: chain O residue 1244 VAL Chi-restraints excluded: chain D residue 85 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 181 optimal weight: 0.6980 chunk 402 optimal weight: 5.9990 chunk 321 optimal weight: 8.9990 chunk 331 optimal weight: 3.9990 chunk 310 optimal weight: 0.5980 chunk 246 optimal weight: 0.4980 chunk 156 optimal weight: 0.4980 chunk 400 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN C 964 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 ASN ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 623 HIS K 845 GLN K1019 GLN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 517 GLN N 686 GLN O 917 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100191 restraints weight = 54501.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.103406 restraints weight = 23137.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105450 restraints weight = 12471.512| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33668 Z= 0.112 Angle : 0.639 19.590 45900 Z= 0.316 Chirality : 0.045 0.561 5124 Planarity : 0.005 0.052 5888 Dihedral : 4.598 36.968 4964 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 5.06 % Allowed : 31.82 % Favored : 63.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.21 (0.13), residues: 4188 helix: 2.92 (0.23), residues: 432 sheet: 0.47 (0.15), residues: 1236 loop : -1.06 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP E 195 HIS 0.019 0.001 HIS J 559 PHE 0.023 0.001 PHE N 715 TYR 0.018 0.001 TYR K 891 ARG 0.011 0.001 ARG B 401 Details of bonding type rmsd link_NAG-ASN : bond 0.01493 ( 12) link_NAG-ASN : angle 6.42297 ( 36) link_BETA1-4 : bond 0.00417 ( 8) link_BETA1-4 : angle 1.51893 ( 24) hydrogen bonds : bond 0.03566 ( 1245) hydrogen bonds : angle 4.51624 ( 3279) SS BOND : bond 0.00289 ( 68) SS BOND : angle 1.55403 ( 136) covalent geometry : bond 0.00255 (33580) covalent geometry : angle 0.60715 (45704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1247 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 1066 time to evaluate : 3.530 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: A 135 LEU cc_start: 0.8310 (mp) cc_final: 0.8033 (mp) REVERT: A 149 VAL cc_start: 0.8835 (t) cc_final: 0.8614 (p) REVERT: B 354 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6916 (t70) REVERT: B 490 GLN cc_start: 0.7672 (mm110) cc_final: 0.7354 (mm110) REVERT: B 504 MET cc_start: 0.7966 (ttm) cc_final: 0.7691 (ttt) REVERT: B 529 LYS cc_start: 0.8156 (ttmm) cc_final: 0.7859 (ptmm) REVERT: B 532 TYR cc_start: 0.7876 (p90) cc_final: 0.7401 (p90) REVERT: B 586 LYS cc_start: 0.8370 (mttm) cc_final: 0.7885 (mtpt) REVERT: B 594 ASP cc_start: 0.7175 (t0) cc_final: 0.6804 (t0) REVERT: B 690 TYR cc_start: 0.8616 (t80) cc_final: 0.8122 (t80) REVERT: C 894 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7776 (mmmm) REVERT: C 904 TRP cc_start: 0.8661 (p-90) cc_final: 0.8429 (p-90) REVERT: C 997 ASP cc_start: 0.7401 (p0) cc_final: 0.7142 (p0) REVERT: C 1009 SER cc_start: 0.8765 (t) cc_final: 0.8427 (p) REVERT: C 1028 LEU cc_start: 0.8585 (tp) cc_final: 0.8347 (tt) REVERT: C 1150 ASN cc_start: 0.7774 (t0) cc_final: 0.7525 (t0) REVERT: C 1225 VAL cc_start: 0.8466 (t) cc_final: 0.8265 (t) REVERT: F 404 ASP cc_start: 0.8092 (t0) cc_final: 0.7883 (t0) REVERT: F 408 ILE cc_start: 0.8324 (mp) cc_final: 0.8104 (mm) REVERT: F 499 GLU cc_start: 0.7608 (pm20) cc_final: 0.7344 (pm20) REVERT: F 679 LYS cc_start: 0.8320 (mmmt) cc_final: 0.7985 (mmmt) REVERT: G 891 TYR cc_start: 0.8501 (t80) cc_final: 0.8271 (t80) REVERT: G 903 MET cc_start: 0.7781 (ttm) cc_final: 0.7352 (mtp) REVERT: G 964 ASN cc_start: 0.8334 (p0) cc_final: 0.7930 (p0) REVERT: G 1029 TYR cc_start: 0.8069 (t80) cc_final: 0.7799 (t80) REVERT: G 1120 THR cc_start: 0.8269 (m) cc_final: 0.7902 (p) REVERT: G 1122 THR cc_start: 0.8669 (p) cc_final: 0.8469 (p) REVERT: I 142 LYS cc_start: 0.8427 (tmmt) cc_final: 0.7835 (tmmt) REVERT: I 195 TRP cc_start: 0.7270 (t60) cc_final: 0.6930 (t60) REVERT: J 371 ARG cc_start: 0.7823 (mtt90) cc_final: 0.7623 (mtt-85) REVERT: J 378 MET cc_start: 0.7869 (mmm) cc_final: 0.7553 (tpp) REVERT: J 399 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8092 (mtmm) REVERT: J 490 GLN cc_start: 0.7680 (tp-100) cc_final: 0.7318 (tp-100) REVERT: J 502 MET cc_start: 0.8038 (mmm) cc_final: 0.7430 (mmm) REVERT: J 569 GLN cc_start: 0.7168 (tp-100) cc_final: 0.6627 (tt0) REVERT: J 641 GLU cc_start: 0.7708 (pt0) cc_final: 0.7409 (pt0) REVERT: J 647 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8121 (m) REVERT: J 679 LYS cc_start: 0.8119 (mmtm) cc_final: 0.7760 (mttm) REVERT: K 1249 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7812 (mm) REVERT: M 113 MET cc_start: 0.5730 (mmm) cc_final: 0.5331 (mmm) REVERT: M 195 TRP cc_start: 0.8528 (t60) cc_final: 0.8108 (t60) REVERT: M 207 PHE cc_start: 0.8408 (m-80) cc_final: 0.8167 (m-10) REVERT: N 376 ASP cc_start: 0.8082 (t0) cc_final: 0.7783 (t0) REVERT: N 393 ASP cc_start: 0.8159 (t0) cc_final: 0.7871 (t0) REVERT: N 399 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7717 (mtpp) REVERT: N 410 ASN cc_start: 0.7778 (m-40) cc_final: 0.7531 (m-40) REVERT: N 459 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7313 (ptm160) REVERT: N 510 ASP cc_start: 0.8553 (t0) cc_final: 0.8305 (t0) REVERT: N 534 CYS cc_start: 0.6202 (m) cc_final: 0.5840 (m) REVERT: N 653 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8542 (m) REVERT: N 727 LYS cc_start: 0.8789 (ttmt) cc_final: 0.8561 (ttmm) REVERT: O 920 GLU cc_start: 0.7650 (pm20) cc_final: 0.7330 (pm20) REVERT: O 928 VAL cc_start: 0.8116 (t) cc_final: 0.7709 (p) REVERT: O 959 VAL cc_start: 0.8399 (p) cc_final: 0.8117 (m) REVERT: O 1035 LYS cc_start: 0.8273 (ttpp) cc_final: 0.7859 (ttmm) REVERT: O 1079 ASN cc_start: 0.8274 (t0) cc_final: 0.8057 (t0) REVERT: O 1096 ASN cc_start: 0.8500 (t0) cc_final: 0.8234 (t0) REVERT: O 1150 ASN cc_start: 0.8333 (t0) cc_final: 0.7990 (t0) REVERT: O 1199 LYS cc_start: 0.8346 (mmmt) cc_final: 0.8000 (mmmt) REVERT: O 1210 SER cc_start: 0.7818 (p) cc_final: 0.7577 (p) outliers start: 181 outliers final: 153 residues processed: 1159 average time/residue: 0.4715 time to fit residues: 865.5964 Evaluate side-chains 1206 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1049 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1153 THR Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 176 HIS Chi-restraints excluded: chain E residue 195 TRP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 583 ARG Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 658 MET Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 713 SER Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1059 LEU Chi-restraints excluded: chain G residue 1112 ILE Chi-restraints excluded: chain G residue 1114 LEU Chi-restraints excluded: chain G residue 1116 CYS Chi-restraints excluded: chain G residue 1144 SER Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1241 LEU Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 186 HIS Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 251 TRP Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 420 THR Chi-restraints excluded: chain J residue 467 GLN Chi-restraints excluded: chain J residue 472 GLU Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 508 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 551 ASN Chi-restraints excluded: chain J residue 561 SER Chi-restraints excluded: chain J residue 567 LYS Chi-restraints excluded: chain J residue 572 SER Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 625 THR Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 653 VAL Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 ILE Chi-restraints excluded: chain J residue 718 CYS Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain J residue 744 LEU Chi-restraints excluded: chain K residue 844 LEU Chi-restraints excluded: chain K residue 960 ASP Chi-restraints excluded: chain K residue 1040 SER Chi-restraints excluded: chain K residue 1046 VAL Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1097 LEU Chi-restraints excluded: chain K residue 1117 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1196 GLU Chi-restraints excluded: chain K residue 1241 LEU Chi-restraints excluded: chain K residue 1249 ILE Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain N residue 394 ASN Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 418 VAL Chi-restraints excluded: chain N residue 435 LEU Chi-restraints excluded: chain N residue 469 VAL Chi-restraints excluded: chain N residue 525 VAL Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 552 THR Chi-restraints excluded: chain N residue 598 CYS Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain N residue 623 HIS Chi-restraints excluded: chain N residue 648 GLU Chi-restraints excluded: chain N residue 653 VAL Chi-restraints excluded: chain N residue 677 GLU Chi-restraints excluded: chain N residue 718 CYS Chi-restraints excluded: chain N residue 743 THR Chi-restraints excluded: chain O residue 923 VAL Chi-restraints excluded: chain O residue 945 LYS Chi-restraints excluded: chain O residue 996 LYS Chi-restraints excluded: chain O residue 1024 GLU Chi-restraints excluded: chain O residue 1040 SER Chi-restraints excluded: chain O residue 1075 GLN Chi-restraints excluded: chain O residue 1105 ILE Chi-restraints excluded: chain O residue 1110 THR Chi-restraints excluded: chain O residue 1115 THR Chi-restraints excluded: chain O residue 1116 CYS Chi-restraints excluded: chain O residue 1132 THR Chi-restraints excluded: chain O residue 1151 VAL Chi-restraints excluded: chain O residue 1156 GLU Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1185 CYS Chi-restraints excluded: chain O residue 1213 VAL Chi-restraints excluded: chain O residue 1244 VAL Chi-restraints excluded: chain D residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 361 optimal weight: 2.9990 chunk 385 optimal weight: 4.9990 chunk 364 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 chunk 315 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 409 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN C 964 ASN ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 892 GLN G1079 ASN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 ASN J 559 HIS J 623 HIS K 845 GLN K1019 GLN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 686 GLN O 917 GLN O 964 ASN O1019 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098043 restraints weight = 54629.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101213 restraints weight = 23329.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103232 restraints weight = 12627.100| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 33668 Z= 0.197 Angle : 0.687 19.717 45900 Z= 0.341 Chirality : 0.047 0.612 5124 Planarity : 0.005 0.054 5888 Dihedral : 4.756 39.492 4964 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.92 % Allowed : 32.23 % Favored : 62.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.32 (0.13), residues: 4188 helix: 2.82 (0.24), residues: 432 sheet: 0.31 (0.15), residues: 1272 loop : -1.09 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 195 HIS 0.021 0.001 HIS J 623 PHE 0.032 0.002 PHE B 570 TYR 0.022 0.002 TYR B 402 ARG 0.009 0.001 ARG K 949 Details of bonding type rmsd link_NAG-ASN : bond 0.01432 ( 12) link_NAG-ASN : angle 6.55013 ( 36) link_BETA1-4 : bond 0.00404 ( 8) link_BETA1-4 : angle 1.42962 ( 24) hydrogen bonds : bond 0.04220 ( 1245) hydrogen bonds : angle 4.59357 ( 3279) SS BOND : bond 0.00487 ( 68) SS BOND : angle 1.94418 ( 136) covalent geometry : bond 0.00459 (33580) covalent geometry : angle 0.65434 (45704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8376 Ramachandran restraints generated. 4188 Oldfield, 0 Emsley, 4188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1228 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 1052 time to evaluate : 3.653 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: symmetry clash REVERT: A 135 LEU cc_start: 0.8398 (mp) cc_final: 0.8190 (mt) REVERT: A 149 VAL cc_start: 0.8827 (t) cc_final: 0.8616 (p) REVERT: B 354 ASP cc_start: 0.7328 (OUTLIER) cc_final: 0.6933 (t70) REVERT: B 384 SER cc_start: 0.8249 (m) cc_final: 0.7786 (p) REVERT: B 490 GLN cc_start: 0.7740 (mm110) cc_final: 0.7409 (mm110) REVERT: B 504 MET cc_start: 0.7983 (ttm) cc_final: 0.7724 (ttt) REVERT: B 544 THR cc_start: 0.7722 (t) cc_final: 0.7447 (m) REVERT: B 586 LYS cc_start: 0.8372 (mttm) cc_final: 0.7923 (mtpt) REVERT: B 594 ASP cc_start: 0.7165 (t0) cc_final: 0.6833 (t0) REVERT: B 658 MET cc_start: 0.7379 (ttp) cc_final: 0.7156 (ttt) REVERT: B 690 TYR cc_start: 0.8484 (t80) cc_final: 0.7954 (t80) REVERT: C 894 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7831 (mmmm) REVERT: C 904 TRP cc_start: 0.8722 (p-90) cc_final: 0.8502 (p-90) REVERT: C 997 ASP cc_start: 0.7405 (p0) cc_final: 0.7142 (p0) REVERT: C 1009 SER cc_start: 0.8789 (t) cc_final: 0.8433 (p) REVERT: C 1028 LEU cc_start: 0.8564 (tp) cc_final: 0.8320 (tt) REVERT: C 1122 THR cc_start: 0.8641 (m) cc_final: 0.8292 (p) REVERT: C 1150 ASN cc_start: 0.7787 (t0) cc_final: 0.7546 (t0) REVERT: F 404 ASP cc_start: 0.8221 (t0) cc_final: 0.8002 (t0) REVERT: F 408 ILE cc_start: 0.8313 (mp) cc_final: 0.8067 (mm) REVERT: F 490 GLN cc_start: 0.7635 (mm-40) cc_final: 0.7425 (mm-40) REVERT: F 499 GLU cc_start: 0.7593 (pm20) cc_final: 0.7349 (pm20) REVERT: G 964 ASN cc_start: 0.8267 (p0) cc_final: 0.7869 (p0) REVERT: G 1029 TYR cc_start: 0.8037 (t80) cc_final: 0.7762 (t80) REVERT: G 1115 THR cc_start: 0.8506 (t) cc_final: 0.8291 (p) REVERT: G 1120 THR cc_start: 0.8276 (m) cc_final: 0.7913 (p) REVERT: G 1122 THR cc_start: 0.8684 (p) cc_final: 0.8470 (p) REVERT: I 142 LYS cc_start: 0.8442 (tmmt) cc_final: 0.7851 (tmmt) REVERT: I 195 TRP cc_start: 0.7392 (t60) cc_final: 0.7122 (t60) REVERT: J 371 ARG cc_start: 0.7956 (mtt90) cc_final: 0.7743 (mtt-85) REVERT: J 378 MET cc_start: 0.7814 (mmm) cc_final: 0.7547 (tpp) REVERT: J 399 LYS cc_start: 0.8484 (mtpp) cc_final: 0.8122 (mtmm) REVERT: J 490 GLN cc_start: 0.7694 (tp-100) cc_final: 0.7351 (tp-100) REVERT: J 502 MET cc_start: 0.8065 (mmm) cc_final: 0.7614 (mmm) REVERT: J 569 GLN cc_start: 0.7289 (tp-100) cc_final: 0.6720 (tt0) REVERT: J 641 GLU cc_start: 0.7707 (pt0) cc_final: 0.7414 (pt0) REVERT: J 679 LYS cc_start: 0.8109 (mmtm) cc_final: 0.7749 (mttm) REVERT: K 1074 CYS cc_start: 0.5901 (m) cc_final: 0.5631 (m) REVERT: K 1249 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7879 (mm) REVERT: M 113 MET cc_start: 0.5806 (mmm) cc_final: 0.5404 (mmm) REVERT: M 195 TRP cc_start: 0.8554 (t60) cc_final: 0.8134 (t60) REVERT: N 376 ASP cc_start: 0.8079 (t0) cc_final: 0.7781 (t0) REVERT: N 393 ASP cc_start: 0.8214 (t0) cc_final: 0.7970 (t0) REVERT: N 459 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7549 (ptm160) REVERT: N 510 ASP cc_start: 0.8587 (t0) cc_final: 0.8313 (t0) REVERT: N 534 CYS cc_start: 0.6342 (m) cc_final: 0.5994 (m) REVERT: N 653 VAL cc_start: 0.8896 (OUTLIER) cc_final: 0.8539 (m) REVERT: N 727 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8560 (ttmm) REVERT: O 920 GLU cc_start: 0.7634 (pm20) cc_final: 0.7280 (pm20) REVERT: O 928 VAL cc_start: 0.8239 (t) cc_final: 0.7863 (p) REVERT: O 959 VAL cc_start: 0.8432 (p) cc_final: 0.8155 (m) REVERT: O 1096 ASN cc_start: 0.8511 (t0) cc_final: 0.8232 (t0) REVERT: O 1150 ASN cc_start: 0.8323 (t0) cc_final: 0.7836 (t0) REVERT: O 1199 LYS cc_start: 0.8344 (mmmt) cc_final: 0.8002 (mmmt) REVERT: O 1210 SER cc_start: 0.7877 (p) cc_final: 0.7553 (p) outliers start: 176 outliers final: 163 residues processed: 1140 average time/residue: 0.4696 time to fit residues: 851.3504 Evaluate side-chains 1211 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 1045 time to evaluate : 3.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 ASN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 ASP Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 524 THR Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 557 GLN Chi-restraints excluded: chain B residue 623 HIS Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 709 LEU Chi-restraints excluded: chain B residue 711 LEU Chi-restraints excluded: chain B residue 720 MET Chi-restraints excluded: chain B residue 748 CYS Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1095 MET Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1153 THR Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1203 VAL Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 176 HIS Chi-restraints excluded: chain E residue 195 TRP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain E residue 264 SER Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 412 VAL Chi-restraints excluded: chain F residue 467 GLN Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 543 THR Chi-restraints excluded: chain F residue 583 ARG Chi-restraints excluded: chain F residue 588 HIS Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 623 HIS Chi-restraints excluded: chain F residue 658 MET Chi-restraints excluded: chain F residue 689 GLN Chi-restraints excluded: chain F residue 709 LEU Chi-restraints excluded: chain F residue 713 SER Chi-restraints excluded: chain F residue 718 CYS Chi-restraints excluded: chain F residue 748 CYS Chi-restraints excluded: chain G residue 1046 VAL Chi-restraints excluded: chain G residue 1059 LEU Chi-restraints excluded: chain G residue 1112 ILE Chi-restraints excluded: chain G residue 1114 LEU Chi-restraints excluded: chain G residue 1116 CYS Chi-restraints excluded: chain G residue 1144 SER Chi-restraints excluded: chain G residue 1156 GLU Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1214 PHE Chi-restraints excluded: chain G residue 1241 LEU Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 168 LEU Chi-restraints excluded: chain I residue 177 MET Chi-restraints excluded: chain I residue 186 HIS Chi-restraints excluded: chain I residue 200 VAL Chi-restraints excluded: chain I residue 221 ARG Chi-restraints excluded: chain I residue 225 ASP Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 251 TRP Chi-restraints excluded: chain J residue 384 SER Chi-restraints excluded: chain J residue 420 THR Chi-restraints excluded: chain J residue 467 GLN Chi-restraints excluded: chain J residue 472 GLU Chi-restraints excluded: chain J residue 486 CYS Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 508 THR Chi-restraints excluded: chain J residue 521 VAL Chi-restraints excluded: chain J residue 534 CYS Chi-restraints excluded: chain J residue 551 ASN Chi-restraints excluded: chain J residue 559 HIS Chi-restraints excluded: chain J residue 561 SER Chi-restraints excluded: chain J residue 567 LYS Chi-restraints excluded: chain J residue 572 SER Chi-restraints excluded: chain J residue 623 HIS Chi-restraints excluded: chain J residue 625 THR Chi-restraints excluded: chain J residue 647 VAL Chi-restraints excluded: chain J residue 648 GLU Chi-restraints excluded: chain J residue 653 VAL Chi-restraints excluded: chain J residue 711 LEU Chi-restraints excluded: chain J residue 714 ILE Chi-restraints excluded: chain J residue 718 CYS Chi-restraints excluded: chain J residue 740 VAL Chi-restraints excluded: chain J residue 744 LEU Chi-restraints excluded: chain K residue 844 LEU Chi-restraints excluded: chain K residue 960 ASP Chi-restraints excluded: chain K residue 971 ILE Chi-restraints excluded: chain K residue 1040 SER Chi-restraints excluded: chain K residue 1046 VAL Chi-restraints excluded: chain K residue 1090 ASN Chi-restraints excluded: chain K residue 1097 LEU Chi-restraints excluded: chain K residue 1100 SER Chi-restraints excluded: chain K residue 1117 THR Chi-restraints excluded: chain K residue 1163 THR Chi-restraints excluded: chain K residue 1196 GLU Chi-restraints excluded: chain K residue 1241 LEU Chi-restraints excluded: chain K residue 1249 ILE Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 200 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR Chi-restraints excluded: chain M residue 253 LYS Chi-restraints excluded: chain N residue 341 VAL Chi-restraints excluded: chain N residue 365 VAL Chi-restraints excluded: chain N residue 387 ILE Chi-restraints excluded: chain N residue 394 ASN Chi-restraints excluded: chain N residue 412 VAL Chi-restraints excluded: chain N residue 469 VAL Chi-restraints excluded: chain N residue 525 VAL Chi-restraints excluded: chain N residue 543 THR Chi-restraints excluded: chain N residue 552 THR Chi-restraints excluded: chain N residue 569 GLN Chi-restraints excluded: chain N residue 598 CYS Chi-restraints excluded: chain N residue 616 THR Chi-restraints excluded: chain N residue 623 HIS Chi-restraints excluded: chain N residue 653 VAL Chi-restraints excluded: chain N residue 677 GLU Chi-restraints excluded: chain N residue 718 CYS Chi-restraints excluded: chain N residue 735 THR Chi-restraints excluded: chain N residue 743 THR Chi-restraints excluded: chain O residue 862 ILE Chi-restraints excluded: chain O residue 923 VAL Chi-restraints excluded: chain O residue 945 LYS Chi-restraints excluded: chain O residue 964 ASN Chi-restraints excluded: chain O residue 996 LYS Chi-restraints excluded: chain O residue 1024 GLU Chi-restraints excluded: chain O residue 1040 SER Chi-restraints excluded: chain O residue 1075 GLN Chi-restraints excluded: chain O residue 1105 ILE Chi-restraints excluded: chain O residue 1110 THR Chi-restraints excluded: chain O residue 1115 THR Chi-restraints excluded: chain O residue 1116 CYS Chi-restraints excluded: chain O residue 1120 THR Chi-restraints excluded: chain O residue 1132 THR Chi-restraints excluded: chain O residue 1151 VAL Chi-restraints excluded: chain O residue 1156 GLU Chi-restraints excluded: chain O residue 1163 THR Chi-restraints excluded: chain O residue 1185 CYS Chi-restraints excluded: chain O residue 1213 VAL Chi-restraints excluded: chain O residue 1244 VAL Chi-restraints excluded: chain D residue 85 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 241 optimal weight: 7.9990 chunk 192 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 200 optimal weight: 80.0000 chunk 118 optimal weight: 8.9990 chunk 246 optimal weight: 0.0070 chunk 78 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 35 optimal weight: 0.0970 chunk 379 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 overall best weight: 3.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN C 964 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 HIS G 892 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS J 623 HIS K 845 GLN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 686 GLN O 917 GLN O 964 ASN O1019 GLN O1146 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.116427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098353 restraints weight = 54459.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.101520 restraints weight = 23165.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.103541 restraints weight = 12519.072| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.114 33668 Z= 0.223 Angle : 0.703 19.857 45900 Z= 0.351 Chirality : 0.048 0.621 5124 Planarity : 0.005 0.054 5888 Dihedral : 4.871 40.533 4964 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.97 % Allowed : 32.29 % Favored : 62.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % 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: -0.38 (0.13), residues: 4188 helix: 2.73 (0.24), residues: 432 sheet: 0.25 (0.15), residues: 1248 loop : -1.11 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 251 HIS 0.032 0.001 HIS J 559 PHE 0.032 0.002 PHE B 570 TYR 0.025 0.002 TYR B 342 ARG 0.011 0.001 ARG B 669 Details of bonding type rmsd link_NAG-ASN : bond 0.01438 ( 12) link_NAG-ASN : angle 6.60520 ( 36) link_BETA1-4 : bond 0.00446 ( 8) link_BETA1-4 : angle 1.45945 ( 24) hydrogen bonds : bond 0.04395 ( 1245) hydrogen bonds : angle 4.64472 ( 3279) SS BOND : bond 0.00461 ( 68) SS BOND : angle 1.98375 ( 136) covalent geometry : bond 0.00517 (33580) covalent geometry : angle 0.66997 (45704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15681.22 seconds wall clock time: 272 minutes 43.92 seconds (16363.92 seconds total)