Starting phenix.real_space_refine on Tue Aug 26 03:04:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x0k_37980/08_2025/8x0k_37980.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x0k_37980/08_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_37980/08_2025/8x0k_37980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x0k_37980/08_2025/8x0k_37980.map" model { file = "/net/cci-nas-00/data/ceres_data/8x0k_37980/08_2025/8x0k_37980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x0k_37980/08_2025/8x0k_37980.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 8.11, per 1000 atoms: 0.25 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: 2.77 Conformation dependent library (CDL) restraints added in 2.3 seconds Enol-peptide restraints added in 1.2 microseconds 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: 1.63 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: 10.05 Time building geometry restraints manager: 3.56 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: 0.01 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: 3.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 34.690 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.900 ------------------------------------------------------------------------------- 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 : 10.38 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG K 949 TYR 0.021 0.002 TYR J 692 PHE 0.031 0.002 PHE C1235 TRP 0.029 0.001 TRP E 195 HIS 0.009 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00420 (33580) covalent geometry : angle 0.71945 (45704) SS BOND : bond 0.00452 ( 68) SS BOND : angle 1.98136 ( 136) hydrogen bonds : bond 0.11916 ( 1245) hydrogen bonds : angle 5.42938 ( 3279) link_BETA1-4 : bond 0.00460 ( 8) link_BETA1-4 : angle 2.19196 ( 24) link_NAG-ASN : bond 0.01461 ( 12) link_NAG-ASN : angle 6.73645 ( 36) *********************** 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 : 1.291 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 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: 0.2181 time to fit residues: 341.0425 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 : 0.895 ------------------------------------------------------------------------------- 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 197 optimal weight: 5.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** J 337 GLN J 340 ASN ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 559 HIS ** K 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 O1002 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.118248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099807 restraints weight = 54857.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103029 restraints weight = 23367.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.105053 restraints weight = 12613.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106363 restraints weight = 8096.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.107191 restraints weight = 5975.800| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.0597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 33668 Z= 0.152 Angle : 0.623 18.958 45900 Z= 0.312 Chirality : 0.046 0.593 5124 Planarity : 0.005 0.083 5888 Dihedral : 5.818 64.000 5007 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.99 % Favored : 95.99 % Rotamer: Outliers : 4.53 % Allowed : 30.92 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.13), residues: 4188 helix: 3.02 (0.24), residues: 432 sheet: 0.33 (0.15), residues: 1200 loop : -1.09 (0.12), residues: 2556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 949 TYR 0.014 0.001 TYR G1057 PHE 0.013 0.001 PHE F 627 TRP 0.025 0.001 TRP E 195 HIS 0.010 0.001 HIS J 559 Details of bonding type rmsd covalent geometry : bond 0.00351 (33580) covalent geometry : angle 0.59363 (45704) SS BOND : bond 0.00325 ( 68) SS BOND : angle 1.26080 ( 136) hydrogen bonds : bond 0.04194 ( 1245) hydrogen bonds : angle 4.82152 ( 3279) link_BETA1-4 : bond 0.00483 ( 8) link_BETA1-4 : angle 1.32139 ( 24) link_NAG-ASN : bond 0.01441 ( 12) link_NAG-ASN : angle 6.33178 ( 36) *********************** 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 1195 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 1033 time to evaluate : 1.043 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 149 VAL cc_start: 0.8468 (t) cc_final: 0.8203 (p) REVERT: B 396 ASP cc_start: 0.8034 (t0) cc_final: 0.7818 (t0) REVERT: B 490 GLN cc_start: 0.7686 (mm110) cc_final: 0.7382 (mm110) REVERT: B 499 GLU cc_start: 0.7333 (pt0) cc_final: 0.6886 (pt0) REVERT: B 502 MET cc_start: 0.7392 (mtp) cc_final: 0.7144 (mtp) REVERT: B 511 ARG cc_start: 0.8669 (tpp80) cc_final: 0.8438 (tpp80) REVERT: B 532 TYR cc_start: 0.8033 (p90) cc_final: 0.7473 (p90) REVERT: B 544 THR cc_start: 0.7572 (t) cc_final: 0.7370 (m) REVERT: B 594 ASP cc_start: 0.7348 (t0) cc_final: 0.6903 (t0) REVERT: B 602 MET cc_start: 0.7863 (mtp) cc_final: 0.7622 (mtt) REVERT: B 669 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7841 (mtt180) REVERT: B 690 TYR cc_start: 0.8567 (t80) cc_final: 0.7782 (t80) REVERT: C 904 TRP cc_start: 0.8651 (p-90) cc_final: 0.8364 (p-90) REVERT: C 1014 ARG cc_start: 0.8580 (mmt180) cc_final: 0.8357 (mmt180) REVERT: C 1242 VAL cc_start: 0.8126 (OUTLIER) cc_final: 0.7862 (p) REVERT: E 186 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.7539 (p-80) REVERT: F 408 ILE cc_start: 0.8139 (mp) cc_final: 0.7848 (mm) REVERT: G 866 TYR cc_start: 0.7677 (p90) cc_final: 0.7332 (p90) REVERT: G 1120 THR cc_start: 0.8090 (m) cc_final: 0.7656 (p) REVERT: J 378 MET cc_start: 0.7849 (mmm) cc_final: 0.7021 (tmm) REVERT: J 396 ASP cc_start: 0.8033 (t0) cc_final: 0.6895 (t0) REVERT: J 399 LYS cc_start: 0.8404 (mtpp) cc_final: 0.7656 (mtmm) REVERT: J 449 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8070 (mt0) REVERT: J 490 GLN cc_start: 0.7422 (tp-100) cc_final: 0.7192 (tp-100) REVERT: J 501 ASP cc_start: 0.7255 (m-30) cc_final: 0.7051 (m-30) REVERT: J 515 SER cc_start: 0.7251 (OUTLIER) cc_final: 0.7033 (p) REVERT: J 679 LYS cc_start: 0.8099 (mmtm) cc_final: 0.7719 (mttm) REVERT: J 717 SER cc_start: 0.8512 (t) cc_final: 0.8114 (t) REVERT: K 903 MET cc_start: 0.7763 (mtp) cc_final: 0.7523 (mtp) REVERT: K 1074 CYS cc_start: 0.5972 (m) cc_final: 0.5680 (m) REVERT: K 1253 ARG cc_start: 0.5572 (OUTLIER) cc_final: 0.5311 (mtt180) REVERT: M 167 ASP cc_start: 0.7935 (t0) cc_final: 0.7649 (t0) REVERT: N 410 ASN cc_start: 0.7978 (m-40) cc_final: 0.7641 (m110) REVERT: N 442 GLU cc_start: 0.7336 (mm-30) cc_final: 0.7030 (mm-30) REVERT: N 529 LYS cc_start: 0.8035 (tptp) cc_final: 0.7826 (tptp) REVERT: N 653 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8617 (m) REVERT: O 920 GLU cc_start: 0.7721 (pm20) cc_final: 0.7412 (pm20) REVERT: O 1043 MET cc_start: 0.7281 (mmm) cc_final: 0.6888 (mmm) REVERT: O 1199 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7899 (mmmt) outliers start: 162 outliers final: 98 residues processed: 1114 average time/residue: 0.1865 time to fit residues: 327.5991 Evaluate side-chains 1108 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 1005 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 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 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 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 186 HIS 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 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 1214 PHE 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 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 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 577 ARG 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 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 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 274 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 377 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 329 optimal weight: 10.0000 chunk 367 optimal weight: 5.9990 chunk 188 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 665 ASN B 673 GLN ** C 915 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 145 HIS ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 386 GLN F 569 GLN F 686 GLN G 833 HIS G1155 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 ASN J 559 HIS J 673 GLN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K1170 HIS ** N 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 686 GLN N 689 GLN ** O 915 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 917 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097479 restraints weight = 54679.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100653 restraints weight = 23290.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102674 restraints weight = 12621.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103949 restraints weight = 8122.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104835 restraints weight = 6007.514| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 33668 Z= 0.255 Angle : 0.668 19.604 45900 Z= 0.338 Chirality : 0.048 0.636 5124 Planarity : 0.005 0.072 5888 Dihedral : 5.609 58.212 4973 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 6.20 % Allowed : 29.36 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.13), residues: 4188 helix: 2.82 (0.24), residues: 432 sheet: 0.20 (0.15), residues: 1192 loop : -1.13 (0.12), residues: 2564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 949 TYR 0.020 0.002 TYR B 690 PHE 0.021 0.002 PHE F 627 TRP 0.029 0.002 TRP E 195 HIS 0.010 0.001 HIS J 559 Details of bonding type rmsd covalent geometry : bond 0.00587 (33580) covalent geometry : angle 0.63911 (45704) SS BOND : bond 0.00494 ( 68) SS BOND : angle 1.47542 ( 136) hydrogen bonds : bond 0.04781 ( 1245) hydrogen bonds : angle 4.84374 ( 3279) link_BETA1-4 : bond 0.00524 ( 8) link_BETA1-4 : angle 1.38608 ( 24) link_NAG-ASN : bond 0.01347 ( 12) link_NAG-ASN : angle 6.45896 ( 36) *********************** 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 1271 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 1049 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 VAL cc_start: 0.8635 (t) cc_final: 0.8405 (p) REVERT: A 201 GLN cc_start: 0.7157 (OUTLIER) cc_final: 0.6943 (pt0) REVERT: B 384 SER cc_start: 0.8223 (m) cc_final: 0.7769 (p) REVERT: B 396 ASP cc_start: 0.8230 (t0) cc_final: 0.7892 (t0) REVERT: B 490 GLN cc_start: 0.7753 (mm110) cc_final: 0.7371 (mm110) REVERT: B 499 GLU cc_start: 0.7325 (pt0) cc_final: 0.5841 (pt0) REVERT: B 532 TYR cc_start: 0.8022 (p90) cc_final: 0.7607 (p90) REVERT: B 586 LYS cc_start: 0.8464 (mttm) cc_final: 0.7461 (mtpt) REVERT: B 594 ASP cc_start: 0.7374 (t0) cc_final: 0.6965 (t0) REVERT: B 690 TYR cc_start: 0.8461 (t80) cc_final: 0.7873 (t80) REVERT: C 904 TRP cc_start: 0.8783 (p-90) cc_final: 0.8554 (p-90) REVERT: C 1014 ARG cc_start: 0.8624 (mmt180) cc_final: 0.8300 (mmt180) REVERT: C 1135 TYR cc_start: 0.8317 (p90) cc_final: 0.7534 (p90) REVERT: E 184 TYR cc_start: 0.7618 (p90) cc_final: 0.7045 (p90) REVERT: E 186 HIS cc_start: 0.8608 (OUTLIER) cc_final: 0.7358 (p-80) REVERT: E 188 LYS cc_start: 0.6125 (mptt) cc_final: 0.5743 (mptt) REVERT: F 376 ASP cc_start: 0.7820 (t0) cc_final: 0.7613 (t0) REVERT: F 408 ILE cc_start: 0.8260 (mp) cc_final: 0.7971 (mm) REVERT: F 430 MET cc_start: 0.7419 (tmm) cc_final: 0.6626 (tmm) REVERT: F 489 TYR cc_start: 0.8358 (m-80) cc_final: 0.7705 (m-80) REVERT: F 594 ASP cc_start: 0.7447 (t0) cc_final: 0.7229 (t0) REVERT: F 651 ILE cc_start: 0.8506 (mm) cc_final: 0.8238 (mt) REVERT: F 679 LYS cc_start: 0.8228 (mmmt) cc_final: 0.7951 (mmmt) REVERT: F 704 VAL cc_start: 0.8406 (t) cc_final: 0.8066 (p) REVERT: G 894 LYS cc_start: 0.7983 (mmtp) cc_final: 0.7690 (mmtp) REVERT: G 1024 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7214 (mm-30) REVERT: G 1120 THR cc_start: 0.8184 (m) cc_final: 0.7788 (p) REVERT: G 1136 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.8073 (mtmm) REVERT: I 142 LYS cc_start: 0.8398 (tmmt) cc_final: 0.7610 (tmmt) REVERT: I 195 TRP cc_start: 0.7173 (t60) cc_final: 0.6860 (t60) REVERT: J 354 ASP cc_start: 0.7587 (t0) cc_final: 0.7103 (t0) REVERT: J 378 MET cc_start: 0.7853 (mmm) cc_final: 0.7079 (mmm) REVERT: J 449 GLN cc_start: 0.8313 (mm-40) cc_final: 0.8099 (mt0) REVERT: J 490 GLN cc_start: 0.7464 (tp-100) cc_final: 0.7125 (tp-100) REVERT: J 502 MET cc_start: 0.7885 (mmm) cc_final: 0.7620 (mmm) REVERT: J 547 ASP cc_start: 0.7380 (t0) cc_final: 0.6978 (t0) REVERT: J 641 GLU cc_start: 0.7753 (pt0) cc_final: 0.7473 (pt0) REVERT: J 679 LYS cc_start: 0.8112 (mmtm) cc_final: 0.7736 (mttm) REVERT: J 717 SER cc_start: 0.8641 (t) cc_final: 0.8331 (t) REVERT: K 903 MET cc_start: 0.7793 (mtp) cc_final: 0.7572 (mtp) REVERT: K 989 ASP cc_start: 0.7620 (m-30) cc_final: 0.7372 (m-30) REVERT: K 1074 CYS cc_start: 0.6067 (m) cc_final: 0.5664 (m) REVERT: K 1253 ARG cc_start: 0.5695 (OUTLIER) cc_final: 0.5438 (mtt180) REVERT: M 113 MET cc_start: 0.5551 (mmm) cc_final: 0.5290 (mmm) REVERT: M 124 LYS cc_start: 0.7872 (tppp) cc_final: 0.7668 (tppp) REVERT: M 167 ASP cc_start: 0.8090 (t0) cc_final: 0.7712 (t0) REVERT: M 195 TRP cc_start: 0.8623 (t60) cc_final: 0.8394 (t60) REVERT: N 396 ASP cc_start: 0.8126 (t0) cc_final: 0.7785 (t0) REVERT: N 399 LYS cc_start: 0.8013 (mtpp) cc_final: 0.7620 (mtpp) REVERT: N 410 ASN cc_start: 0.7964 (m-40) cc_final: 0.7684 (m-40) REVERT: N 459 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7631 (ptm160) REVERT: N 529 LYS cc_start: 0.8136 (tptp) cc_final: 0.7767 (tptp) REVERT: N 534 CYS cc_start: 0.6136 (m) cc_final: 0.5749 (m) REVERT: N 653 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8652 (m) REVERT: N 727 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8595 (ttmm) REVERT: O 920 GLU cc_start: 0.7727 (pm20) cc_final: 0.7406 (pm20) REVERT: O 1079 ASN cc_start: 0.8334 (t0) cc_final: 0.8049 (t0) REVERT: O 1150 ASN cc_start: 0.8426 (t0) cc_final: 0.8082 (t0) REVERT: O 1199 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7895 (mmmt) outliers start: 222 outliers final: 171 residues processed: 1162 average time/residue: 0.1886 time to fit residues: 345.1461 Evaluate side-chains 1211 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 1035 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 201 GLN 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 363 SER Chi-restraints excluded: chain B residue 387 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 THR 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 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 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 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 1106 VAL Chi-restraints excluded: chain C residue 1153 THR Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 111 MET 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 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 363 SER Chi-restraints excluded: chain F residue 426 VAL Chi-restraints excluded: chain F residue 512 THR Chi-restraints excluded: chain F residue 543 THR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 561 SER Chi-restraints excluded: chain F residue 583 ARG 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 720 MET Chi-restraints excluded: chain G residue 862 ILE Chi-restraints excluded: chain G residue 982 SER 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 1097 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 1158 THR Chi-restraints excluded: chain G residue 1185 CYS Chi-restraints excluded: chain G residue 1202 ILE Chi-restraints excluded: chain G residue 1213 VAL Chi-restraints excluded: chain G residue 1214 PHE Chi-restraints excluded: chain G residue 1222 LEU Chi-restraints excluded: chain G residue 1241 LEU Chi-restraints excluded: chain G residue 1248 CYS Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 173 ILE 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 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 420 THR Chi-restraints excluded: chain J residue 467 GLN 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 559 HIS Chi-restraints excluded: chain J residue 561 SER 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 821 VAL Chi-restraints excluded: chain K residue 844 LEU Chi-restraints excluded: chain K residue 864 CYS Chi-restraints excluded: chain K residue 875 VAL 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 1105 ILE Chi-restraints excluded: chain K residue 1117 THR Chi-restraints excluded: chain K residue 1134 THR Chi-restraints excluded: chain K residue 1142 ASP Chi-restraints excluded: chain K residue 1181 VAL Chi-restraints excluded: chain K residue 1196 GLU Chi-restraints excluded: chain K residue 1241 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 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 543 THR Chi-restraints excluded: chain N residue 560 VAL 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 658 MET Chi-restraints excluded: chain N residue 708 LEU 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 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 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 1116 CYS Chi-restraints excluded: chain O residue 1120 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 Chi-restraints excluded: chain O residue 1251 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 262 optimal weight: 0.3980 chunk 233 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 405 optimal weight: 7.9990 chunk 372 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 chunk 348 optimal weight: 4.9990 chunk 281 optimal weight: 0.9990 chunk 315 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- 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 545 ASN G1079 ASN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 ASN J 337 GLN J 340 ASN J 467 GLN J 559 HIS K1090 ASN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 337 GLN N 340 ASN N 686 GLN O 917 GLN O1226 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.118084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.099732 restraints weight = 54272.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102935 restraints weight = 23042.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104965 restraints weight = 12442.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106229 restraints weight = 7991.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107097 restraints weight = 5911.518| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33668 Z= 0.122 Angle : 0.609 18.807 45900 Z= 0.304 Chirality : 0.046 0.583 5124 Planarity : 0.005 0.066 5888 Dihedral : 5.135 59.720 4970 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 5.73 % Allowed : 30.00 % Favored : 64.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.13), residues: 4188 helix: 2.95 (0.24), residues: 432 sheet: 0.50 (0.15), residues: 1172 loop : -1.10 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 243 TYR 0.013 0.001 TYR B 690 PHE 0.021 0.001 PHE N 339 TRP 0.021 0.001 TRP E 195 HIS 0.010 0.001 HIS J 559 Details of bonding type rmsd covalent geometry : bond 0.00279 (33580) covalent geometry : angle 0.57922 (45704) SS BOND : bond 0.00335 ( 68) SS BOND : angle 1.43018 ( 136) hydrogen bonds : bond 0.03853 ( 1245) hydrogen bonds : angle 4.66175 ( 3279) link_BETA1-4 : bond 0.00439 ( 8) link_BETA1-4 : angle 1.47615 ( 24) link_NAG-ASN : bond 0.01371 ( 12) link_NAG-ASN : angle 6.20339 ( 36) *********************** 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 1267 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 1062 time to evaluate : 1.306 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 135 LEU cc_start: 0.8402 (mp) cc_final: 0.8189 (mt) REVERT: A 149 VAL cc_start: 0.8667 (t) cc_final: 0.8439 (p) REVERT: B 354 ASP cc_start: 0.7334 (OUTLIER) cc_final: 0.7012 (t70) REVERT: B 396 ASP cc_start: 0.8082 (t0) cc_final: 0.7812 (t0) REVERT: B 399 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8230 (mtpt) REVERT: B 401 ARG cc_start: 0.8422 (ptt180) cc_final: 0.7783 (ptt180) REVERT: B 490 GLN cc_start: 0.7716 (mm110) cc_final: 0.7326 (mm-40) REVERT: B 532 TYR cc_start: 0.7990 (p90) cc_final: 0.7526 (p90) REVERT: B 543 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7774 (m) REVERT: B 575 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8236 (m) REVERT: B 586 LYS cc_start: 0.8460 (mttm) cc_final: 0.7948 (mtpt) REVERT: B 594 ASP cc_start: 0.7352 (t0) cc_final: 0.7069 (t0) REVERT: B 690 TYR cc_start: 0.8600 (t80) cc_final: 0.7964 (t80) REVERT: C 894 LYS cc_start: 0.8184 (mmtm) cc_final: 0.7802 (mmmm) REVERT: C 904 TRP cc_start: 0.8693 (p-90) cc_final: 0.8483 (p-90) REVERT: C 1135 TYR cc_start: 0.8220 (p90) cc_final: 0.7433 (p90) REVERT: E 184 TYR cc_start: 0.7545 (p90) cc_final: 0.6943 (p90) REVERT: E 186 HIS cc_start: 0.8634 (OUTLIER) cc_final: 0.7475 (p-80) REVERT: F 376 ASP cc_start: 0.7836 (t0) cc_final: 0.7597 (t0) REVERT: F 408 ILE cc_start: 0.8387 (mp) cc_final: 0.8114 (mm) REVERT: F 430 MET cc_start: 0.7409 (tmm) cc_final: 0.6742 (tmm) REVERT: F 679 LYS cc_start: 0.8280 (mmmt) cc_final: 0.7962 (mmmt) REVERT: G 894 LYS cc_start: 0.7941 (mmtp) cc_final: 0.7652 (mmtp) REVERT: G 903 MET cc_start: 0.7815 (ttm) cc_final: 0.7385 (mtp) REVERT: G 1029 TYR cc_start: 0.7999 (t80) cc_final: 0.7752 (t80) REVERT: G 1120 THR cc_start: 0.8178 (m) cc_final: 0.7765 (p) REVERT: I 142 LYS cc_start: 0.8397 (tmmt) cc_final: 0.7559 (tmmt) REVERT: I 180 ASP cc_start: 0.7935 (p0) cc_final: 0.7401 (p0) REVERT: J 354 ASP cc_start: 0.7521 (t0) cc_final: 0.6998 (t0) REVERT: J 378 MET cc_start: 0.7828 (mmm) cc_final: 0.7015 (mmm) REVERT: J 399 LYS cc_start: 0.8461 (mtpp) cc_final: 0.8059 (mtmm) REVERT: J 490 GLN cc_start: 0.7493 (tp-100) cc_final: 0.7133 (tp-100) REVERT: J 502 MET cc_start: 0.7948 (mmm) cc_final: 0.7580 (mmm) REVERT: J 532 TYR cc_start: 0.8365 (p90) cc_final: 0.8036 (p90) REVERT: J 548 MET cc_start: 0.7116 (mmm) cc_final: 0.6889 (mmm) REVERT: J 641 GLU cc_start: 0.7729 (pt0) cc_final: 0.7470 (pt0) REVERT: J 679 LYS cc_start: 0.8111 (mmtm) cc_final: 0.7742 (mttm) REVERT: J 717 SER cc_start: 0.8511 (t) cc_final: 0.8255 (t) REVERT: K 903 MET cc_start: 0.7739 (mtp) cc_final: 0.7523 (mtp) REVERT: K 952 TYR cc_start: 0.7584 (p90) cc_final: 0.7348 (p90) REVERT: K 989 ASP cc_start: 0.7620 (m-30) cc_final: 0.7297 (m-30) REVERT: K 1172 SER cc_start: 0.8172 (t) cc_final: 0.7601 (p) REVERT: M 113 MET cc_start: 0.5494 (mmm) cc_final: 0.5195 (mmm) REVERT: M 124 LYS cc_start: 0.7796 (tppp) cc_final: 0.7553 (tppp) REVERT: M 195 TRP cc_start: 0.8571 (t60) cc_final: 0.8216 (t60) REVERT: N 351 TYR cc_start: 0.7607 (t80) cc_final: 0.7129 (t80) REVERT: N 459 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7628 (ptm160) REVERT: N 516 GLN cc_start: 0.8722 (mm110) cc_final: 0.8497 (mm-40) REVERT: N 529 LYS cc_start: 0.8049 (tptp) cc_final: 0.7638 (tptp) REVERT: N 586 LYS cc_start: 0.8428 (ttmm) cc_final: 0.8165 (mtpp) REVERT: N 653 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8640 (m) REVERT: O 920 GLU cc_start: 0.7621 (pm20) cc_final: 0.7377 (pm20) REVERT: O 1079 ASN cc_start: 0.8278 (t0) cc_final: 0.7999 (t0) REVERT: O 1096 ASN cc_start: 0.8549 (t0) cc_final: 0.8304 (t0) REVERT: O 1150 ASN cc_start: 0.8388 (t0) cc_final: 0.8140 (t0) REVERT: O 1199 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7885 (mmmt) REVERT: O 1235 PHE cc_start: 0.8107 (t80) cc_final: 0.7648 (t80) outliers start: 205 outliers final: 145 residues processed: 1163 average time/residue: 0.2095 time to fit residues: 383.9478 Evaluate side-chains 1200 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 1050 time to evaluate : 1.253 ------------------------------------------------------------------------------- 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 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 500 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 543 THR Chi-restraints excluded: chain B residue 575 VAL 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 748 CYS Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 910 PHE 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 1163 THR Chi-restraints excluded: chain C residue 1185 CYS Chi-restraints excluded: chain C residue 1232 LEU Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 111 MET 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 467 GLN Chi-restraints excluded: chain F residue 484 ILE Chi-restraints excluded: chain F residue 561 SER 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 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 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 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 534 CYS 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 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 1097 LEU Chi-restraints excluded: chain K residue 1100 SER 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 1163 THR 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 231 VAL Chi-restraints excluded: chain M residue 250 THR 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 469 VAL Chi-restraints excluded: chain N residue 487 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 560 VAL Chi-restraints excluded: chain N residue 569 GLN Chi-restraints excluded: chain N residue 653 VAL Chi-restraints excluded: chain N residue 709 LEU 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 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 1115 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 1226 GLN 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 186 optimal weight: 0.0020 chunk 154 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 243 optimal weight: 0.9980 chunk 264 optimal weight: 5.9990 chunk 360 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 114 optimal weight: 6.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 GLN ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN B 686 GLN ** 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 337 GLN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 517 GLN N 686 GLN O 917 GLN O 964 ASN O1226 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.118264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099905 restraints weight = 54583.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103091 restraints weight = 23291.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.105110 restraints weight = 12616.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106299 restraints weight = 8119.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.107221 restraints weight = 6073.701| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33668 Z= 0.118 Angle : 0.602 18.751 45900 Z= 0.299 Chirality : 0.045 0.570 5124 Planarity : 0.005 0.064 5888 Dihedral : 4.849 47.418 4968 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.06 % Favored : 95.92 % Rotamer: Outliers : 5.87 % Allowed : 30.45 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.13), residues: 4188 helix: 2.92 (0.23), residues: 432 sheet: 0.41 (0.15), residues: 1220 loop : -1.05 (0.12), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K1253 TYR 0.019 0.001 TYR F 402 PHE 0.019 0.001 PHE N 715 TRP 0.020 0.001 TRP E 195 HIS 0.007 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00272 (33580) covalent geometry : angle 0.57187 (45704) SS BOND : bond 0.00353 ( 68) SS BOND : angle 1.50856 ( 136) hydrogen bonds : bond 0.03699 ( 1245) hydrogen bonds : angle 4.55709 ( 3279) link_BETA1-4 : bond 0.00367 ( 8) link_BETA1-4 : angle 1.44580 ( 24) link_NAG-ASN : bond 0.01337 ( 12) link_NAG-ASN : angle 6.09245 ( 36) *********************** 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 1267 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 1057 time to evaluate : 1.338 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 135 LEU cc_start: 0.8342 (mp) cc_final: 0.8057 (mp) REVERT: A 149 VAL cc_start: 0.8661 (t) cc_final: 0.8443 (p) REVERT: A 193 TYR cc_start: 0.8237 (m-80) cc_final: 0.7782 (m-80) REVERT: B 354 ASP cc_start: 0.7322 (OUTLIER) cc_final: 0.6986 (t70) REVERT: B 396 ASP cc_start: 0.8025 (t0) cc_final: 0.7779 (t0) REVERT: B 399 LYS cc_start: 0.8521 (mtpp) cc_final: 0.8224 (mtpt) REVERT: B 490 GLN cc_start: 0.7722 (mm110) cc_final: 0.7354 (mm110) REVERT: B 504 MET cc_start: 0.7986 (ttm) cc_final: 0.7705 (ttt) REVERT: B 510 ASP cc_start: 0.8189 (t0) cc_final: 0.7976 (t0) REVERT: B 532 TYR cc_start: 0.7984 (p90) cc_final: 0.7495 (p90) REVERT: B 543 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7785 (m) REVERT: B 575 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8220 (m) REVERT: B 586 LYS cc_start: 0.8424 (mttm) cc_final: 0.7942 (mtpt) REVERT: B 594 ASP cc_start: 0.7325 (t0) cc_final: 0.7031 (t0) REVERT: B 665 ASN cc_start: 0.8218 (m-40) cc_final: 0.7954 (m-40) REVERT: B 690 TYR cc_start: 0.8626 (t80) cc_final: 0.8015 (t80) REVERT: C 894 LYS cc_start: 0.8159 (mmtm) cc_final: 0.7781 (mmmm) REVERT: C 904 TRP cc_start: 0.8663 (p-90) cc_final: 0.8425 (p-90) REVERT: C 1014 ARG cc_start: 0.8593 (mmt180) cc_final: 0.8318 (mmt180) REVERT: C 1135 TYR cc_start: 0.8202 (p90) cc_final: 0.7473 (p90) REVERT: C 1225 VAL cc_start: 0.8484 (t) cc_final: 0.8280 (t) REVERT: E 186 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.7152 (p-80) REVERT: F 376 ASP cc_start: 0.7873 (t0) cc_final: 0.7548 (t0) REVERT: F 408 ILE cc_start: 0.8381 (mp) cc_final: 0.8123 (mm) REVERT: F 430 MET cc_start: 0.7429 (tmm) cc_final: 0.6804 (tmm) REVERT: F 679 LYS cc_start: 0.8280 (mmmt) cc_final: 0.7927 (mmmt) REVERT: G 894 LYS cc_start: 0.7959 (mmtp) cc_final: 0.7673 (mmtp) REVERT: G 903 MET cc_start: 0.7778 (ttm) cc_final: 0.7346 (mtp) REVERT: G 964 ASN cc_start: 0.8352 (p0) cc_final: 0.7956 (p0) REVERT: G 1120 THR cc_start: 0.8194 (m) cc_final: 0.7784 (p) REVERT: G 1122 THR cc_start: 0.8596 (p) cc_final: 0.8369 (p) REVERT: I 142 LYS cc_start: 0.8433 (tmmt) cc_final: 0.7674 (tmmt) REVERT: I 180 ASP cc_start: 0.7974 (p0) cc_final: 0.7476 (p0) REVERT: J 354 ASP cc_start: 0.7462 (t0) cc_final: 0.6972 (t0) REVERT: J 378 MET cc_start: 0.7825 (mmm) cc_final: 0.7002 (mmm) REVERT: J 399 LYS cc_start: 0.8461 (mtpp) cc_final: 0.7656 (mtmm) REVERT: J 490 GLN cc_start: 0.7526 (tp-100) cc_final: 0.7234 (tp-100) REVERT: J 502 MET cc_start: 0.8006 (mmm) cc_final: 0.7491 (mmm) REVERT: J 641 GLU cc_start: 0.7722 (pt0) cc_final: 0.7479 (pt0) REVERT: J 679 LYS cc_start: 0.8113 (mmtm) cc_final: 0.7753 (mttm) REVERT: K 952 TYR cc_start: 0.7612 (p90) cc_final: 0.7345 (p90) REVERT: K 1074 CYS cc_start: 0.5827 (m) cc_final: 0.5577 (m) REVERT: K 1093 VAL cc_start: 0.8892 (p) cc_final: 0.8668 (p) REVERT: K 1249 ILE cc_start: 0.8097 (OUTLIER) cc_final: 0.7770 (mm) REVERT: M 113 MET cc_start: 0.5474 (mmm) cc_final: 0.5214 (mmm) REVERT: M 124 LYS cc_start: 0.7831 (tppp) cc_final: 0.7547 (tppp) REVERT: M 167 ASP cc_start: 0.7941 (t0) cc_final: 0.7711 (t70) REVERT: M 188 LYS cc_start: 0.8959 (ttmm) cc_final: 0.8571 (ttmm) REVERT: M 195 TRP cc_start: 0.8587 (t60) cc_final: 0.8075 (t60) REVERT: N 351 TYR cc_start: 0.7523 (t80) cc_final: 0.6986 (t80) REVERT: N 459 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7622 (ptm160) REVERT: N 516 GLN cc_start: 0.8725 (mm110) cc_final: 0.8475 (mm-40) REVERT: N 529 LYS cc_start: 0.8053 (tptp) cc_final: 0.7592 (tptp) REVERT: N 586 LYS cc_start: 0.8400 (ttmm) cc_final: 0.8168 (mmmm) REVERT: N 609 ILE cc_start: 0.8462 (mt) cc_final: 0.8257 (mm) REVERT: N 653 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8549 (m) REVERT: O 920 GLU cc_start: 0.7613 (pm20) cc_final: 0.7344 (pm20) REVERT: O 959 VAL cc_start: 0.8425 (p) cc_final: 0.8164 (m) REVERT: O 1035 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7783 (ttmm) REVERT: O 1096 ASN cc_start: 0.8541 (t0) cc_final: 0.8288 (t0) REVERT: O 1150 ASN cc_start: 0.8418 (t0) cc_final: 0.8112 (t0) REVERT: O 1199 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7907 (mmmt) REVERT: O 1235 PHE cc_start: 0.8059 (t80) cc_final: 0.7653 (t80) outliers start: 210 outliers final: 161 residues processed: 1167 average time/residue: 0.1993 time to fit residues: 368.9009 Evaluate side-chains 1191 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1024 time to evaluate : 1.272 ------------------------------------------------------------------------------- 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 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 429 THR Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 500 ILE 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 575 VAL 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 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 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 E residue 111 MET 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 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 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 971 ILE 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 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 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 467 GLN 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 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 822 MET 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 1097 LEU Chi-restraints excluded: chain K residue 1100 SER Chi-restraints excluded: chain K residue 1105 ILE Chi-restraints excluded: chain K residue 1117 THR Chi-restraints excluded: chain K residue 1134 THR Chi-restraints excluded: chain K residue 1163 THR 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 215 LYS Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR 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 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 588 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 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 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 1115 THR Chi-restraints excluded: chain O residue 1116 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 99 optimal weight: 5.9990 chunk 156 optimal weight: 0.0970 chunk 194 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 291 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 360 optimal weight: 8.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 ASN G1001 ASN G1155 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 337 GLN J 467 GLN K1019 GLN K1075 GLN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 686 GLN O 917 GLN O1226 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.117400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.099145 restraints weight = 54668.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.102332 restraints weight = 23322.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.104341 restraints weight = 12630.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105617 restraints weight = 8140.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.106451 restraints weight = 6035.681| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1518 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= 0.159 Angle : 0.625 18.794 45900 Z= 0.311 Chirality : 0.046 0.593 5124 Planarity : 0.005 0.058 5888 Dihedral : 4.822 50.085 4966 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.25 % Favored : 95.73 % Rotamer: Outliers : 6.03 % Allowed : 30.20 % Favored : 63.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.13), residues: 4188 helix: 2.92 (0.23), residues: 432 sheet: 0.30 (0.15), residues: 1268 loop : -1.00 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1038 TYR 0.020 0.002 TYR F 402 PHE 0.021 0.001 PHE N 715 TRP 0.021 0.001 TRP E 195 HIS 0.009 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00369 (33580) covalent geometry : angle 0.59514 (45704) SS BOND : bond 0.00422 ( 68) SS BOND : angle 1.61108 ( 136) hydrogen bonds : bond 0.03964 ( 1245) hydrogen bonds : angle 4.55636 ( 3279) link_BETA1-4 : bond 0.00375 ( 8) link_BETA1-4 : angle 1.43098 ( 24) link_NAG-ASN : bond 0.01292 ( 12) link_NAG-ASN : angle 6.13280 ( 36) *********************** 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 1247 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1031 time to evaluate : 1.215 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: A 135 LEU cc_start: 0.8393 (mp) cc_final: 0.8180 (mt) REVERT: A 149 VAL cc_start: 0.8795 (t) cc_final: 0.8561 (p) REVERT: B 354 ASP cc_start: 0.7326 (OUTLIER) cc_final: 0.6985 (t70) REVERT: B 396 ASP cc_start: 0.7955 (t0) cc_final: 0.7693 (t0) REVERT: B 417 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7805 (mtmm) REVERT: B 490 GLN cc_start: 0.7760 (mm110) cc_final: 0.7406 (mm110) REVERT: B 504 MET cc_start: 0.7987 (ttm) cc_final: 0.7728 (ttt) REVERT: B 510 ASP cc_start: 0.8211 (t0) cc_final: 0.7960 (t0) REVERT: B 532 TYR cc_start: 0.7994 (p90) cc_final: 0.7500 (p90) REVERT: B 543 THR cc_start: 0.8109 (OUTLIER) cc_final: 0.7909 (m) REVERT: B 575 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8241 (m) REVERT: B 586 LYS cc_start: 0.8415 (mttm) cc_final: 0.7921 (mtpt) REVERT: B 594 ASP cc_start: 0.7293 (t0) cc_final: 0.7023 (t0) REVERT: B 690 TYR cc_start: 0.8530 (t80) cc_final: 0.7922 (t80) REVERT: C 894 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7795 (mmmm) REVERT: C 904 TRP cc_start: 0.8701 (p-90) cc_final: 0.8478 (p-90) REVERT: C 1014 ARG cc_start: 0.8630 (mmt180) cc_final: 0.8378 (mmt180) REVERT: C 1135 TYR cc_start: 0.8218 (p90) cc_final: 0.7546 (p90) REVERT: E 184 TYR cc_start: 0.7540 (p90) cc_final: 0.7022 (p90) REVERT: F 376 ASP cc_start: 0.7892 (t0) cc_final: 0.7527 (t0) REVERT: F 408 ILE cc_start: 0.8353 (mp) cc_final: 0.8107 (mm) REVERT: F 430 MET cc_start: 0.7457 (tmm) cc_final: 0.7027 (tmm) REVERT: F 679 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7936 (mmmt) REVERT: G 894 LYS cc_start: 0.8007 (mmtp) cc_final: 0.7706 (mmtp) REVERT: G 903 MET cc_start: 0.7892 (ttm) cc_final: 0.7437 (mtp) REVERT: G 1029 TYR cc_start: 0.8036 (t80) cc_final: 0.7734 (t80) REVERT: G 1115 THR cc_start: 0.8509 (t) cc_final: 0.8299 (p) REVERT: G 1120 THR cc_start: 0.8213 (m) cc_final: 0.7837 (p) REVERT: G 1122 THR cc_start: 0.8620 (p) cc_final: 0.8387 (p) REVERT: I 142 LYS cc_start: 0.8444 (tmmt) cc_final: 0.7684 (tmmt) REVERT: I 180 ASP cc_start: 0.8062 (p0) cc_final: 0.7696 (p0) REVERT: J 378 MET cc_start: 0.7798 (mmm) cc_final: 0.7504 (tpp) REVERT: J 399 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8136 (mtmm) REVERT: J 490 GLN cc_start: 0.7544 (tp-100) cc_final: 0.7226 (tp-100) REVERT: J 502 MET cc_start: 0.8051 (mmm) cc_final: 0.7697 (mmm) REVERT: J 641 GLU cc_start: 0.7720 (pt0) cc_final: 0.7395 (pt0) REVERT: J 679 LYS cc_start: 0.8120 (mmtm) cc_final: 0.7755 (mttm) REVERT: K 952 TYR cc_start: 0.7673 (p90) cc_final: 0.7399 (p90) REVERT: K 1074 CYS cc_start: 0.5909 (m) cc_final: 0.5587 (m) REVERT: K 1093 VAL cc_start: 0.8893 (p) cc_final: 0.8675 (p) REVERT: K 1249 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7822 (mm) REVERT: M 113 MET cc_start: 0.5531 (mmm) cc_final: 0.5232 (mmm) REVERT: M 124 LYS cc_start: 0.7864 (tppp) cc_final: 0.7562 (tppp) REVERT: M 145 HIS cc_start: 0.7841 (p90) cc_final: 0.7631 (p90) REVERT: M 195 TRP cc_start: 0.8575 (t60) cc_final: 0.8106 (t60) REVERT: N 351 TYR cc_start: 0.7716 (t80) cc_final: 0.7205 (t80) REVERT: N 459 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7557 (ptm160) REVERT: N 529 LYS cc_start: 0.8154 (tptp) cc_final: 0.7674 (tptp) REVERT: N 609 ILE cc_start: 0.8481 (mt) cc_final: 0.8273 (mm) REVERT: N 653 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8645 (m) REVERT: N 727 LYS cc_start: 0.8793 (ttmt) cc_final: 0.8560 (ttmm) REVERT: O 920 GLU cc_start: 0.7613 (pm20) cc_final: 0.7348 (pm20) REVERT: O 959 VAL cc_start: 0.8456 (p) cc_final: 0.8179 (m) REVERT: O 1079 ASN cc_start: 0.8306 (t0) cc_final: 0.8075 (t0) REVERT: O 1096 ASN cc_start: 0.8530 (t0) cc_final: 0.8251 (t0) REVERT: O 1107 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: O 1150 ASN cc_start: 0.8356 (t0) cc_final: 0.7996 (t0) REVERT: O 1199 LYS cc_start: 0.8238 (mmmt) cc_final: 0.7867 (mmmt) REVERT: O 1235 PHE cc_start: 0.8146 (t80) cc_final: 0.7672 (t80) outliers start: 216 outliers final: 182 residues processed: 1146 average time/residue: 0.1799 time to fit residues: 329.5099 Evaluate side-chains 1207 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 1019 time to evaluate : 1.234 ------------------------------------------------------------------------------- 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 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 429 THR Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 500 ILE 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 575 VAL 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 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 1232 LEU 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 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 493 THR Chi-restraints excluded: chain F residue 543 THR Chi-restraints excluded: chain F residue 544 THR Chi-restraints excluded: chain F residue 561 SER 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 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 926 SER Chi-restraints excluded: chain G residue 971 ILE 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 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 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 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 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 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 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 1097 LEU Chi-restraints excluded: chain K residue 1100 SER Chi-restraints excluded: chain K residue 1105 ILE Chi-restraints excluded: chain K residue 1117 THR Chi-restraints excluded: chain K residue 1134 THR Chi-restraints excluded: chain K residue 1139 LYS Chi-restraints excluded: chain K residue 1163 THR 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 215 LYS Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR Chi-restraints excluded: chain N residue 341 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 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 588 HIS Chi-restraints excluded: chain N residue 616 THR 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 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 933 HIS 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 1226 GLN 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 266 optimal weight: 0.1980 chunk 253 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 304 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 chunk 395 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 124 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN C 964 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 432 HIS G 967 HIS I 172 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 337 GLN ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1019 GLN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 516 GLN N 517 GLN N 686 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 = 0.3474 r_free = 0.3474 target = 0.117999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099673 restraints weight = 54679.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102906 restraints weight = 23162.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104943 restraints weight = 12385.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106244 restraints weight = 7954.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.107021 restraints weight = 5867.649| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33668 Z= 0.131 Angle : 0.621 18.545 45900 Z= 0.308 Chirality : 0.046 0.582 5124 Planarity : 0.004 0.056 5888 Dihedral : 4.733 51.807 4966 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.11 % Favored : 95.87 % Rotamer: Outliers : 6.20 % Allowed : 30.42 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.13), residues: 4188 helix: 2.94 (0.23), residues: 432 sheet: 0.32 (0.15), residues: 1260 loop : -0.98 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 669 TYR 0.019 0.001 TYR F 402 PHE 0.021 0.001 PHE N 715 TRP 0.021 0.001 TRP E 195 HIS 0.008 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00306 (33580) covalent geometry : angle 0.59201 (45704) SS BOND : bond 0.00320 ( 68) SS BOND : angle 1.59767 ( 136) hydrogen bonds : bond 0.03758 ( 1245) hydrogen bonds : angle 4.51069 ( 3279) link_BETA1-4 : bond 0.00381 ( 8) link_BETA1-4 : angle 1.46676 ( 24) link_NAG-ASN : bond 0.01300 ( 12) link_NAG-ASN : angle 6.03563 ( 36) *********************** 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 1257 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 222 poor density : 1035 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8386 (mp) cc_final: 0.8079 (mp) REVERT: A 149 VAL cc_start: 0.8817 (t) cc_final: 0.8585 (p) REVERT: B 354 ASP cc_start: 0.7315 (OUTLIER) cc_final: 0.6953 (t70) REVERT: B 368 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7589 (tp30) REVERT: B 396 ASP cc_start: 0.7888 (t0) cc_final: 0.7616 (t0) REVERT: B 450 ASP cc_start: 0.7164 (t0) cc_final: 0.6853 (t0) REVERT: B 490 GLN cc_start: 0.7763 (mm110) cc_final: 0.7416 (mm110) REVERT: B 504 MET cc_start: 0.8007 (ttm) cc_final: 0.7732 (ttt) REVERT: B 510 ASP cc_start: 0.8208 (t0) cc_final: 0.7691 (t0) REVERT: B 513 LEU cc_start: 0.8386 (mt) cc_final: 0.8150 (mt) REVERT: B 544 THR cc_start: 0.7517 (t) cc_final: 0.7292 (m) REVERT: B 575 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8224 (m) REVERT: B 586 LYS cc_start: 0.8389 (mttm) cc_final: 0.7908 (mtmt) REVERT: B 594 ASP cc_start: 0.7304 (t0) cc_final: 0.7023 (t0) REVERT: B 658 MET cc_start: 0.7500 (tmm) cc_final: 0.7273 (ttp) REVERT: B 690 TYR cc_start: 0.8629 (t80) cc_final: 0.8052 (t80) REVERT: C 894 LYS cc_start: 0.8195 (mmtm) cc_final: 0.7801 (mmmm) REVERT: C 904 TRP cc_start: 0.8691 (p-90) cc_final: 0.8483 (p-90) REVERT: C 1014 ARG cc_start: 0.8680 (mmt180) cc_final: 0.8461 (mmt180) REVERT: C 1135 TYR cc_start: 0.8174 (p90) cc_final: 0.7538 (p90) REVERT: C 1225 VAL cc_start: 0.8470 (t) cc_final: 0.8267 (t) REVERT: E 139 LYS cc_start: 0.7877 (mptt) cc_final: 0.7347 (mppt) REVERT: F 376 ASP cc_start: 0.7907 (t0) cc_final: 0.7498 (t0) REVERT: F 381 ILE cc_start: 0.8423 (mt) cc_final: 0.8205 (mp) REVERT: F 408 ILE cc_start: 0.8344 (mp) cc_final: 0.8099 (mm) REVERT: F 430 MET cc_start: 0.7455 (tmm) cc_final: 0.7044 (tmm) REVERT: F 679 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7864 (mmmt) REVERT: G 894 LYS cc_start: 0.7997 (mmtp) cc_final: 0.7775 (mmtp) REVERT: G 903 MET cc_start: 0.7868 (ttm) cc_final: 0.7407 (mtp) REVERT: G 964 ASN cc_start: 0.8397 (p0) cc_final: 0.7954 (p0) REVERT: G 1029 TYR cc_start: 0.8038 (t80) cc_final: 0.7738 (t80) REVERT: G 1120 THR cc_start: 0.8231 (m) cc_final: 0.7862 (p) REVERT: G 1122 THR cc_start: 0.8658 (p) cc_final: 0.8439 (p) REVERT: I 142 LYS cc_start: 0.8430 (tmmt) cc_final: 0.7825 (tmmt) REVERT: I 180 ASP cc_start: 0.8068 (p0) cc_final: 0.7801 (p0) REVERT: J 378 MET cc_start: 0.7795 (mmm) cc_final: 0.7488 (tpp) REVERT: J 399 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8126 (mtmm) REVERT: J 490 GLN cc_start: 0.7562 (tp-100) cc_final: 0.7243 (tp-100) REVERT: J 502 MET cc_start: 0.8048 (mmm) cc_final: 0.7660 (mmm) REVERT: J 641 GLU cc_start: 0.7718 (pt0) cc_final: 0.7495 (pt0) REVERT: J 679 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7759 (mttm) REVERT: K 952 TYR cc_start: 0.7629 (p90) cc_final: 0.7300 (p90) REVERT: K 1074 CYS cc_start: 0.5883 (m) cc_final: 0.5584 (m) REVERT: K 1249 ILE cc_start: 0.8179 (OUTLIER) cc_final: 0.7832 (mm) REVERT: M 113 MET cc_start: 0.5524 (mmm) cc_final: 0.5228 (mmm) REVERT: M 124 LYS cc_start: 0.7852 (tppp) cc_final: 0.7558 (tppp) REVERT: M 145 HIS cc_start: 0.7887 (p90) cc_final: 0.7679 (p90) REVERT: M 195 TRP cc_start: 0.8585 (t60) cc_final: 0.8145 (t60) REVERT: N 351 TYR cc_start: 0.7689 (t80) cc_final: 0.7177 (t80) REVERT: N 401 ARG cc_start: 0.8344 (ptt180) cc_final: 0.8127 (ptt90) REVERT: N 410 ASN cc_start: 0.7792 (m-40) cc_final: 0.7538 (m-40) REVERT: N 459 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7510 (ptm160) REVERT: N 504 MET cc_start: 0.7793 (tpp) cc_final: 0.7586 (tpp) REVERT: N 534 CYS cc_start: 0.6141 (m) cc_final: 0.5738 (m) REVERT: N 653 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8503 (m) REVERT: N 664 ASN cc_start: 0.8742 (OUTLIER) cc_final: 0.8327 (m-40) REVERT: N 727 LYS cc_start: 0.8782 (ttmt) cc_final: 0.8550 (ttmm) REVERT: O 920 GLU cc_start: 0.7593 (pm20) cc_final: 0.7292 (pm20) REVERT: O 959 VAL cc_start: 0.8439 (p) cc_final: 0.8165 (m) REVERT: O 1079 ASN cc_start: 0.8293 (t0) cc_final: 0.8059 (t0) REVERT: O 1096 ASN cc_start: 0.8516 (t0) cc_final: 0.8241 (t0) REVERT: O 1107 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7133 (pm20) REVERT: O 1150 ASN cc_start: 0.8347 (t0) cc_final: 0.7951 (t0) REVERT: O 1199 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7879 (mmmt) REVERT: O 1235 PHE cc_start: 0.8120 (t80) cc_final: 0.7670 (t80) outliers start: 222 outliers final: 179 residues processed: 1153 average time/residue: 0.1894 time to fit residues: 348.2111 Evaluate side-chains 1203 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 1018 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 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 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 429 THR Chi-restraints excluded: chain B residue 467 GLN Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 531 LYS Chi-restraints excluded: chain B residue 535 THR Chi-restraints excluded: chain B residue 546 SER Chi-restraints excluded: chain B residue 575 VAL 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 966 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 1232 LEU Chi-restraints excluded: chain C residue 1240 ILE Chi-restraints excluded: chain C residue 1242 VAL Chi-restraints excluded: chain E residue 111 MET Chi-restraints excluded: chain E residue 175 VAL 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 561 SER 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 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 850 GLU Chi-restraints excluded: chain G residue 926 SER Chi-restraints excluded: chain G residue 971 ILE 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 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 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 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 567 LYS Chi-restraints excluded: chain J residue 572 SER 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 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 1190 THR 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 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 512 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 653 VAL Chi-restraints excluded: chain N residue 664 ASN 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 933 HIS Chi-restraints excluded: chain O residue 945 LYS 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 1232 LEU 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 47 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 chunk 257 optimal weight: 0.3980 chunk 310 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 206 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 96 optimal weight: 0.0070 overall best weight: 0.8402 ------------------------------------------------------------------------------- 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 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 337 GLN J 467 GLN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 516 GLN N 686 GLN O 917 GLN O 964 ASN O1226 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.119052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100709 restraints weight = 54486.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103942 restraints weight = 23162.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105978 restraints weight = 12482.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.107254 restraints weight = 8000.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108124 restraints weight = 5898.824| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.1702 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= 0.109 Angle : 0.616 18.184 45900 Z= 0.304 Chirality : 0.045 0.563 5124 Planarity : 0.004 0.052 5888 Dihedral : 4.591 51.245 4966 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.72 % Favored : 96.25 % Rotamer: Outliers : 5.34 % Allowed : 31.34 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.13), residues: 4188 helix: 3.02 (0.23), residues: 432 sheet: 0.35 (0.15), residues: 1256 loop : -0.94 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 949 TYR 0.018 0.001 TYR F 402 PHE 0.023 0.001 PHE N 715 TRP 0.029 0.001 TRP A 251 HIS 0.012 0.001 HIS N 395 Details of bonding type rmsd covalent geometry : bond 0.00250 (33580) covalent geometry : angle 0.58849 (45704) SS BOND : bond 0.00275 ( 68) SS BOND : angle 1.49065 ( 136) hydrogen bonds : bond 0.03436 ( 1245) hydrogen bonds : angle 4.45758 ( 3279) link_BETA1-4 : bond 0.00399 ( 8) link_BETA1-4 : angle 1.51854 ( 24) link_NAG-ASN : bond 0.01300 ( 12) link_NAG-ASN : angle 5.90355 ( 36) *********************** 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 1248 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 1057 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8296 (mp) cc_final: 0.8000 (mp) REVERT: A 149 VAL cc_start: 0.8792 (t) cc_final: 0.8579 (p) REVERT: B 354 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6890 (t70) REVERT: B 368 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7578 (mm-30) REVERT: B 396 ASP cc_start: 0.7822 (t0) cc_final: 0.7583 (t0) REVERT: B 399 LYS cc_start: 0.8416 (mtpp) cc_final: 0.8171 (mtpp) REVERT: B 401 ARG cc_start: 0.8575 (ptt180) cc_final: 0.8240 (ptt180) REVERT: B 490 GLN cc_start: 0.7763 (mm110) cc_final: 0.7425 (mm110) REVERT: B 504 MET cc_start: 0.7988 (ttm) cc_final: 0.7714 (ttt) REVERT: B 510 ASP cc_start: 0.8156 (t0) cc_final: 0.7635 (t0) REVERT: B 532 TYR cc_start: 0.7912 (p90) cc_final: 0.7405 (p90) REVERT: B 575 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8199 (m) REVERT: B 594 ASP cc_start: 0.7305 (t0) cc_final: 0.7019 (t0) REVERT: B 690 TYR cc_start: 0.8655 (t80) cc_final: 0.8082 (t80) REVERT: C 904 TRP cc_start: 0.8663 (p-90) cc_final: 0.8443 (p-90) REVERT: C 1009 SER cc_start: 0.8774 (t) cc_final: 0.8413 (p) REVERT: C 1135 TYR cc_start: 0.8146 (p90) cc_final: 0.7551 (p90) REVERT: F 376 ASP cc_start: 0.7903 (t0) cc_final: 0.7525 (t0) REVERT: F 408 ILE cc_start: 0.8310 (mp) cc_final: 0.8091 (mm) REVERT: F 651 ILE cc_start: 0.8408 (mm) cc_final: 0.8130 (mt) REVERT: F 679 LYS cc_start: 0.8215 (mmmt) cc_final: 0.7846 (mmmt) REVERT: G 894 LYS cc_start: 0.7984 (mmtp) cc_final: 0.7668 (mmtp) REVERT: G 903 MET cc_start: 0.7739 (ttm) cc_final: 0.7302 (mtp) REVERT: G 964 ASN cc_start: 0.8372 (p0) cc_final: 0.7910 (p0) REVERT: G 1029 TYR cc_start: 0.8092 (t80) cc_final: 0.7806 (t80) REVERT: G 1120 THR cc_start: 0.8230 (m) cc_final: 0.7869 (p) REVERT: G 1122 THR cc_start: 0.8651 (p) cc_final: 0.8444 (p) REVERT: G 1138 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8251 (p0) REVERT: I 142 LYS cc_start: 0.8412 (tmmt) cc_final: 0.7803 (tmmt) REVERT: I 180 ASP cc_start: 0.8048 (p0) cc_final: 0.7789 (p0) REVERT: J 378 MET cc_start: 0.7796 (mmm) cc_final: 0.7540 (tpp) REVERT: J 399 LYS cc_start: 0.8519 (mtpp) cc_final: 0.8116 (mtmm) REVERT: J 490 GLN cc_start: 0.7579 (tp-100) cc_final: 0.7241 (tp-100) REVERT: J 502 MET cc_start: 0.8053 (mmm) cc_final: 0.7427 (mmm) REVERT: J 641 GLU cc_start: 0.7721 (pt0) cc_final: 0.7486 (pt0) REVERT: J 679 LYS cc_start: 0.8104 (mmtm) cc_final: 0.7742 (mttm) REVERT: K 952 TYR cc_start: 0.7557 (p90) cc_final: 0.7273 (p90) REVERT: K 1031 ASN cc_start: 0.8638 (t0) cc_final: 0.8222 (t0) REVERT: K 1074 CYS cc_start: 0.5884 (m) cc_final: 0.5593 (m) REVERT: K 1249 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7802 (mm) REVERT: M 113 MET cc_start: 0.5547 (mmm) cc_final: 0.5256 (mmm) REVERT: M 124 LYS cc_start: 0.7833 (tppp) cc_final: 0.7523 (tppp) REVERT: M 167 ASP cc_start: 0.7939 (t70) cc_final: 0.7739 (t70) REVERT: M 195 TRP cc_start: 0.8570 (t60) cc_final: 0.8160 (t60) REVERT: M 207 PHE cc_start: 0.8407 (m-80) cc_final: 0.8144 (m-10) REVERT: N 351 TYR cc_start: 0.7554 (t80) cc_final: 0.7045 (t80) REVERT: N 401 ARG cc_start: 0.8307 (ptt180) cc_final: 0.7995 (ptt90) REVERT: N 459 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7484 (ptm160) REVERT: N 534 CYS cc_start: 0.6189 (m) cc_final: 0.5810 (m) REVERT: N 653 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8465 (m) REVERT: N 664 ASN cc_start: 0.8721 (OUTLIER) cc_final: 0.8334 (m-40) REVERT: N 727 LYS cc_start: 0.8770 (ttmt) cc_final: 0.8547 (ttmm) REVERT: O 920 GLU cc_start: 0.7541 (pm20) cc_final: 0.7248 (pm20) REVERT: O 928 VAL cc_start: 0.8127 (t) cc_final: 0.7734 (p) REVERT: O 959 VAL cc_start: 0.8391 (p) cc_final: 0.8113 (m) REVERT: O 1096 ASN cc_start: 0.8500 (t0) cc_final: 0.8241 (t0) REVERT: O 1107 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7129 (pm20) REVERT: O 1150 ASN cc_start: 0.8299 (t0) cc_final: 0.7866 (t0) REVERT: O 1199 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7919 (mmmt) REVERT: O 1235 PHE cc_start: 0.8087 (t80) cc_final: 0.7679 (t80) outliers start: 191 outliers final: 157 residues processed: 1158 average time/residue: 0.1793 time to fit residues: 329.4150 Evaluate side-chains 1208 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 1044 time to evaluate : 1.037 ------------------------------------------------------------------------------- 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 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 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 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 546 SER Chi-restraints excluded: chain B residue 575 VAL 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 748 CYS Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 966 ASP 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 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 412 VAL Chi-restraints excluded: chain F residue 493 THR Chi-restraints excluded: chain F residue 561 SER 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 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 926 SER Chi-restraints excluded: chain G residue 1023 VAL 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 1138 ASP 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 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 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 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 822 MET 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 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 215 LYS Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR 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 531 LYS 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 648 GLU 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 386 optimal weight: 6.9990 chunk 217 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 314 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 288 optimal weight: 1.9990 chunk 338 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 328 optimal weight: 6.9990 chunk 310 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS ** 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 C1146 HIS ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1001 ASN I 172 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 337 GLN ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1067 ASN K1085 ASN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 410 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** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099330 restraints weight = 54425.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.102544 restraints weight = 23261.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104527 restraints weight = 12588.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105864 restraints weight = 8114.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.106552 restraints weight = 5986.691| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 33668 Z= 0.151 Angle : 0.651 18.701 45900 Z= 0.321 Chirality : 0.046 0.594 5124 Planarity : 0.005 0.051 5888 Dihedral : 4.650 55.553 4966 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.39 % Allowed : 31.28 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.13), residues: 4188 helix: 3.00 (0.23), residues: 432 sheet: 0.31 (0.15), residues: 1260 loop : -0.96 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 949 TYR 0.020 0.002 TYR F 402 PHE 0.026 0.002 PHE N 339 TRP 0.021 0.001 TRP E 195 HIS 0.017 0.001 HIS N 395 Details of bonding type rmsd covalent geometry : bond 0.00352 (33580) covalent geometry : angle 0.61979 (45704) SS BOND : bond 0.00403 ( 68) SS BOND : angle 1.76288 ( 136) hydrogen bonds : bond 0.03817 ( 1245) hydrogen bonds : angle 4.48269 ( 3279) link_BETA1-4 : bond 0.00353 ( 8) link_BETA1-4 : angle 1.45889 ( 24) link_NAG-ASN : bond 0.01403 ( 12) link_NAG-ASN : angle 6.26076 ( 36) *********************** 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 1248 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 1055 time to evaluate : 0.871 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 135 LEU cc_start: 0.8309 (mp) cc_final: 0.8039 (mp) REVERT: A 149 VAL cc_start: 0.8856 (t) cc_final: 0.8643 (p) REVERT: B 396 ASP cc_start: 0.7894 (t0) cc_final: 0.7670 (t0) REVERT: B 399 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8249 (mtpp) REVERT: B 401 ARG cc_start: 0.8561 (ptt180) cc_final: 0.8217 (ptt180) REVERT: B 450 ASP cc_start: 0.7147 (t0) cc_final: 0.6842 (t0) REVERT: B 490 GLN cc_start: 0.7763 (mm110) cc_final: 0.7379 (mm110) REVERT: B 504 MET cc_start: 0.7995 (ttm) cc_final: 0.7708 (ttt) REVERT: B 529 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7873 (ptmm) REVERT: B 544 THR cc_start: 0.7848 (t) cc_final: 0.7480 (m) REVERT: B 575 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8200 (m) REVERT: B 586 LYS cc_start: 0.8345 (mttm) cc_final: 0.7877 (mtpt) REVERT: B 594 ASP cc_start: 0.7317 (t0) cc_final: 0.6891 (t0) REVERT: B 690 TYR cc_start: 0.8629 (t80) cc_final: 0.8064 (t80) REVERT: C 904 TRP cc_start: 0.8695 (p-90) cc_final: 0.8487 (p-90) REVERT: C 1009 SER cc_start: 0.8795 (t) cc_final: 0.8414 (p) REVERT: C 1135 TYR cc_start: 0.8172 (p90) cc_final: 0.7550 (p90) REVERT: E 139 LYS cc_start: 0.7892 (mptt) cc_final: 0.7344 (mppt) REVERT: F 376 ASP cc_start: 0.7916 (t0) cc_final: 0.7498 (t0) REVERT: F 408 ILE cc_start: 0.8286 (mp) cc_final: 0.8070 (mm) REVERT: F 679 LYS cc_start: 0.8212 (mmmt) cc_final: 0.7879 (mmmt) REVERT: G 903 MET cc_start: 0.7833 (ttm) cc_final: 0.7388 (mtp) REVERT: G 964 ASN cc_start: 0.8396 (p0) cc_final: 0.7963 (p0) REVERT: G 1029 TYR cc_start: 0.8095 (t80) cc_final: 0.7760 (t80) REVERT: G 1120 THR cc_start: 0.8270 (m) cc_final: 0.7900 (p) REVERT: G 1122 THR cc_start: 0.8661 (p) cc_final: 0.8448 (p) REVERT: G 1138 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8278 (p0) REVERT: I 142 LYS cc_start: 0.8417 (tmmt) cc_final: 0.7802 (tmmt) REVERT: J 378 MET cc_start: 0.7807 (mmm) cc_final: 0.7529 (tpp) REVERT: J 399 LYS cc_start: 0.8486 (mtpp) cc_final: 0.8089 (mtmm) REVERT: J 490 GLN cc_start: 0.7636 (tp-100) cc_final: 0.7312 (tp-100) REVERT: J 502 MET cc_start: 0.8065 (mmm) cc_final: 0.7512 (mmm) REVERT: J 641 GLU cc_start: 0.7727 (pt0) cc_final: 0.7500 (pt0) REVERT: J 679 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7731 (mttm) REVERT: K 952 TYR cc_start: 0.7569 (p90) cc_final: 0.7206 (p90) REVERT: K 991 LYS cc_start: 0.8332 (mttt) cc_final: 0.8098 (mttp) REVERT: K 1031 ASN cc_start: 0.8662 (t0) cc_final: 0.8227 (t0) REVERT: K 1074 CYS cc_start: 0.5891 (m) cc_final: 0.5592 (m) REVERT: K 1249 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7842 (mm) REVERT: M 113 MET cc_start: 0.5569 (mmm) cc_final: 0.5255 (mmm) REVERT: M 124 LYS cc_start: 0.7860 (tppp) cc_final: 0.7563 (tppp) REVERT: M 195 TRP cc_start: 0.8583 (t60) cc_final: 0.8151 (t60) REVERT: N 351 TYR cc_start: 0.7731 (t80) cc_final: 0.7188 (t80) REVERT: N 399 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7892 (mtpp) REVERT: N 459 ARG cc_start: 0.7967 (ttm-80) cc_final: 0.7476 (ptp-110) REVERT: N 504 MET cc_start: 0.7799 (tpp) cc_final: 0.7313 (mpp) REVERT: N 534 CYS cc_start: 0.6203 (m) cc_final: 0.5834 (m) REVERT: N 547 ASP cc_start: 0.8154 (m-30) cc_final: 0.7531 (t0) REVERT: N 586 LYS cc_start: 0.8522 (mttp) cc_final: 0.8123 (mmmm) REVERT: N 653 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8490 (m) REVERT: N 664 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8330 (m-40) REVERT: O 920 GLU cc_start: 0.7554 (pm20) cc_final: 0.7285 (pm20) REVERT: O 928 VAL cc_start: 0.8251 (t) cc_final: 0.7844 (p) REVERT: O 959 VAL cc_start: 0.8406 (p) cc_final: 0.8128 (m) REVERT: O 1079 ASN cc_start: 0.8300 (t0) cc_final: 0.8072 (t0) REVERT: O 1096 ASN cc_start: 0.8501 (t0) cc_final: 0.8239 (t0) REVERT: O 1107 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7184 (pm20) REVERT: O 1150 ASN cc_start: 0.8271 (t0) cc_final: 0.7826 (t0) REVERT: O 1199 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7920 (mmmt) REVERT: O 1235 PHE cc_start: 0.8114 (t80) cc_final: 0.7790 (t80) outliers start: 193 outliers final: 175 residues processed: 1154 average time/residue: 0.1775 time to fit residues: 325.5242 Evaluate side-chains 1231 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 1050 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 168 LEU 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 387 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 493 THR 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 575 VAL 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 748 CYS Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 966 ASP 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 1107 GLU 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 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 467 GLN Chi-restraints excluded: chain F residue 493 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 817 GLU Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 862 ILE Chi-restraints excluded: chain G residue 926 SER Chi-restraints excluded: chain G residue 982 SER Chi-restraints excluded: chain G residue 1023 VAL 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 1138 ASP 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 1185 CYS Chi-restraints excluded: chain G residue 1217 MET 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 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 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 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 844 LEU Chi-restraints excluded: chain K residue 944 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 1084 MET 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 1190 THR Chi-restraints excluded: chain K residue 1196 GLU Chi-restraints excluded: chain K residue 1226 GLN 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 215 LYS Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR 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 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 569 GLN Chi-restraints excluded: chain N residue 598 CYS Chi-restraints excluded: chain N residue 648 GLU 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 718 CYS Chi-restraints excluded: chain N residue 735 THR Chi-restraints excluded: chain N residue 743 THR Chi-restraints excluded: chain O residue 923 VAL Chi-restraints excluded: chain O residue 933 HIS Chi-restraints excluded: chain O residue 945 LYS 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 125 optimal weight: 20.0000 chunk 96 optimal weight: 0.0070 chunk 54 optimal weight: 5.9990 chunk 198 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 326 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 389 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- 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 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN C 964 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS G1079 ASN I 172 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 337 GLN ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1085 ASN ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 686 GLN O 917 GLN ** O 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099385 restraints weight = 54802.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102597 restraints weight = 23258.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104640 restraints weight = 12535.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.105889 restraints weight = 8030.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106784 restraints weight = 5928.427| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 33668 Z= 0.170 Angle : 0.741 59.200 45900 Z= 0.387 Chirality : 0.046 0.594 5124 Planarity : 0.005 0.051 5888 Dihedral : 4.650 55.578 4966 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 5.28 % Allowed : 32.04 % Favored : 62.68 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.13), residues: 4188 helix: 3.01 (0.23), residues: 432 sheet: 0.31 (0.15), residues: 1260 loop : -0.96 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG C1014 TYR 0.019 0.002 TYR F 402 PHE 0.033 0.002 PHE B 570 TRP 0.021 0.001 TRP E 195 HIS 0.015 0.001 HIS E 176 Details of bonding type rmsd covalent geometry : bond 0.00406 (33580) covalent geometry : angle 0.71376 (45704) SS BOND : bond 0.00413 ( 68) SS BOND : angle 1.84993 ( 136) hydrogen bonds : bond 0.03810 ( 1245) hydrogen bonds : angle 4.48982 ( 3279) link_BETA1-4 : bond 0.00350 ( 8) link_BETA1-4 : angle 1.44324 ( 24) link_NAG-ASN : bond 0.01275 ( 12) link_NAG-ASN : angle 6.30079 ( 36) ********************** 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 1229 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 1040 time to evaluate : 1.235 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 135 LEU cc_start: 0.8311 (mp) cc_final: 0.8041 (mp) REVERT: A 149 VAL cc_start: 0.8857 (t) cc_final: 0.8644 (p) REVERT: B 396 ASP cc_start: 0.7894 (t0) cc_final: 0.7646 (t0) REVERT: B 401 ARG cc_start: 0.8558 (ptt180) cc_final: 0.8232 (ptt180) REVERT: B 450 ASP cc_start: 0.7143 (t0) cc_final: 0.6844 (t0) REVERT: B 490 GLN cc_start: 0.7761 (mm110) cc_final: 0.7385 (mm110) REVERT: B 504 MET cc_start: 0.7979 (ttm) cc_final: 0.7704 (ttt) REVERT: B 529 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7876 (ptmm) REVERT: B 544 THR cc_start: 0.7762 (t) cc_final: 0.7487 (m) REVERT: B 575 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8198 (m) REVERT: B 586 LYS cc_start: 0.8347 (mttm) cc_final: 0.7876 (mtpt) REVERT: B 594 ASP cc_start: 0.7322 (t0) cc_final: 0.6892 (t0) REVERT: B 669 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7748 (mtt90) REVERT: B 679 LYS cc_start: 0.7996 (mmmt) cc_final: 0.7747 (mmmm) REVERT: B 690 TYR cc_start: 0.8629 (t80) cc_final: 0.8077 (t80) REVERT: C 904 TRP cc_start: 0.8690 (p-90) cc_final: 0.8484 (p-90) REVERT: C 1009 SER cc_start: 0.8797 (t) cc_final: 0.8414 (p) REVERT: C 1135 TYR cc_start: 0.8174 (p90) cc_final: 0.7546 (p90) REVERT: E 139 LYS cc_start: 0.7902 (mptt) cc_final: 0.7346 (mppt) REVERT: F 376 ASP cc_start: 0.7904 (t0) cc_final: 0.7500 (t0) REVERT: F 679 LYS cc_start: 0.8211 (mmmt) cc_final: 0.7876 (mmmt) REVERT: G 903 MET cc_start: 0.7837 (ttm) cc_final: 0.7387 (mtp) REVERT: G 964 ASN cc_start: 0.8395 (p0) cc_final: 0.7954 (p0) REVERT: G 1029 TYR cc_start: 0.8087 (t80) cc_final: 0.7763 (t80) REVERT: G 1120 THR cc_start: 0.8264 (m) cc_final: 0.7898 (p) REVERT: G 1122 THR cc_start: 0.8657 (p) cc_final: 0.8449 (p) REVERT: G 1138 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8283 (p0) REVERT: I 142 LYS cc_start: 0.8417 (tmmt) cc_final: 0.7809 (tmmt) REVERT: I 172 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6823 (mp-120) REVERT: J 378 MET cc_start: 0.7804 (mmm) cc_final: 0.7533 (tpp) REVERT: J 399 LYS cc_start: 0.8451 (mtpp) cc_final: 0.8093 (mtmm) REVERT: J 490 GLN cc_start: 0.7633 (tp-100) cc_final: 0.7313 (tp-100) REVERT: J 502 MET cc_start: 0.8062 (mmm) cc_final: 0.7508 (mmm) REVERT: J 641 GLU cc_start: 0.7727 (pt0) cc_final: 0.7504 (pt0) REVERT: J 679 LYS cc_start: 0.8099 (mmtm) cc_final: 0.7753 (mttm) REVERT: K 952 TYR cc_start: 0.7560 (p90) cc_final: 0.7208 (p90) REVERT: K 1074 CYS cc_start: 0.5880 (m) cc_final: 0.5590 (m) REVERT: K 1249 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7840 (mm) REVERT: M 113 MET cc_start: 0.5554 (mmm) cc_final: 0.5250 (mmm) REVERT: M 124 LYS cc_start: 0.7853 (tppp) cc_final: 0.7567 (tppp) REVERT: M 195 TRP cc_start: 0.8577 (t60) cc_final: 0.8152 (t60) REVERT: N 351 TYR cc_start: 0.7723 (t80) cc_final: 0.7185 (t80) REVERT: N 399 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7890 (mtpp) REVERT: N 459 ARG cc_start: 0.7958 (ttm-80) cc_final: 0.7474 (ptp-110) REVERT: N 504 MET cc_start: 0.7772 (tpp) cc_final: 0.7295 (mpp) REVERT: N 534 CYS cc_start: 0.6189 (m) cc_final: 0.5823 (m) REVERT: N 547 ASP cc_start: 0.8140 (m-30) cc_final: 0.7533 (t0) REVERT: N 586 LYS cc_start: 0.8518 (mttp) cc_final: 0.8115 (mmmm) REVERT: N 653 VAL cc_start: 0.8858 (OUTLIER) cc_final: 0.8490 (m) REVERT: N 664 ASN cc_start: 0.8699 (OUTLIER) cc_final: 0.8330 (m-40) REVERT: O 920 GLU cc_start: 0.7552 (pm20) cc_final: 0.7283 (pm20) REVERT: O 928 VAL cc_start: 0.8232 (t) cc_final: 0.7840 (p) REVERT: O 959 VAL cc_start: 0.8407 (p) cc_final: 0.8126 (m) REVERT: O 1079 ASN cc_start: 0.8301 (t0) cc_final: 0.8072 (t0) REVERT: O 1096 ASN cc_start: 0.8501 (t0) cc_final: 0.8231 (t0) REVERT: O 1107 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: O 1150 ASN cc_start: 0.8268 (t0) cc_final: 0.7822 (t0) REVERT: O 1199 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7919 (mmmt) REVERT: O 1235 PHE cc_start: 0.8107 (t80) cc_final: 0.7792 (t80) outliers start: 189 outliers final: 179 residues processed: 1136 average time/residue: 0.1802 time to fit residues: 325.8227 Evaluate side-chains 1227 residues out of total 3580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 1041 time to evaluate : 0.855 ------------------------------------------------------------------------------- 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 168 LEU 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 387 ILE Chi-restraints excluded: chain B residue 412 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 493 THR 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 575 VAL 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 748 CYS Chi-restraints excluded: chain C residue 875 VAL Chi-restraints excluded: chain C residue 966 ASP 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 1107 GLU 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 158 LEU 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 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 561 SER 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 817 GLU Chi-restraints excluded: chain G residue 850 GLU Chi-restraints excluded: chain G residue 862 ILE Chi-restraints excluded: chain G residue 926 SER Chi-restraints excluded: chain G residue 971 ILE Chi-restraints excluded: chain G residue 1023 VAL 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 1138 ASP 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 1217 MET 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 172 GLN 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 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 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 844 LEU Chi-restraints excluded: chain K residue 944 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 1084 MET 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 1226 GLN 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 215 LYS Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 250 THR 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 512 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 569 GLN Chi-restraints excluded: chain N residue 598 CYS Chi-restraints excluded: chain N residue 648 GLU 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 718 CYS Chi-restraints excluded: chain N residue 735 THR Chi-restraints excluded: chain N residue 743 THR Chi-restraints excluded: chain O residue 923 VAL Chi-restraints excluded: chain O residue 933 HIS Chi-restraints excluded: chain O residue 945 LYS 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 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 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 390 optimal weight: 1.9990 chunk 335 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 325 optimal weight: 8.9990 chunk 341 optimal weight: 0.9980 chunk 33 optimal weight: 0.0070 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 288 optimal weight: 3.9990 chunk 263 optimal weight: 30.0000 chunk 324 optimal weight: 4.9990 overall best weight: 2.2004 ------------------------------------------------------------------------------- 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 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN C 964 ASN ** E 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 892 GLN I 172 GLN ** I 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 337 GLN ** J 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 517 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 686 GLN O 917 GLN ** O 964 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099437 restraints weight = 54872.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102660 restraints weight = 23304.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104706 restraints weight = 12577.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.106008 restraints weight = 8040.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106830 restraints weight = 5914.913| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.211 33668 Z= 0.202 Angle : 0.813 59.200 45900 Z= 0.444 Chirality : 0.046 0.595 5124 Planarity : 0.005 0.050 5888 Dihedral : 4.647 55.593 4966 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 5.50 % Allowed : 31.84 % Favored : 62.65 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.13), residues: 4188 helix: 3.01 (0.23), residues: 432 sheet: 0.31 (0.15), residues: 1260 loop : -0.96 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C1014 TYR 0.018 0.002 TYR F 402 PHE 0.031 0.002 PHE B 570 TRP 0.021 0.001 TRP E 195 HIS 0.016 0.001 HIS E 176 Details of bonding type rmsd covalent geometry : bond 0.00453 (33580) covalent geometry : angle 0.78756 (45704) SS BOND : bond 0.00417 ( 68) SS BOND : angle 1.90452 ( 136) hydrogen bonds : bond 0.03813 ( 1245) hydrogen bonds : angle 4.48912 ( 3279) link_BETA1-4 : bond 0.00341 ( 8) link_BETA1-4 : angle 1.43792 ( 24) link_NAG-ASN : bond 0.01271 ( 12) link_NAG-ASN : angle 6.30234 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7754.87 seconds wall clock time: 133 minutes 38.83 seconds (8018.83 seconds total)