Starting phenix.real_space_refine on Sun Feb 8 05:59:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bnd_44724/02_2026/9bnd_44724.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bnd_44724/02_2026/9bnd_44724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bnd_44724/02_2026/9bnd_44724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bnd_44724/02_2026/9bnd_44724.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bnd_44724/02_2026/9bnd_44724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bnd_44724/02_2026/9bnd_44724.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 193 5.16 5 C 25698 2.51 5 N 6633 2.21 5 O 7742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40266 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 5327 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 652, 5313 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 621} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 652, 5313 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 621} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 5445 Chain: "B" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7825 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 5331 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 652, 5313 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 621} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Conformer: "B" Number of residues, atoms: 652, 5313 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 621} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 bond proxies already assigned to first conformer: 5439 Chain: "D" Number of atoms: 7825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7825 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 7 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 5320 Number of conformers: 3 Conformer: "A" Number of residues, atoms: 652, 5314 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 621} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 652, 5314 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 621} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 5458 Conformer: "C" Number of residues, atoms: 652, 5314 Classifications: {'peptide': 652} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 621} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 5458 Chain: "F" Number of atoms: 7840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7840 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 54, 'TRANS': 951} Chain breaks: 7 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" 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: "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: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 13.81, per 1000 atoms: 0.34 Number of scatterers: 40266 At special positions: 0 Unit cell: (168.896, 176.384, 227.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 193 16.00 O 7742 8.00 N 6633 7.00 C 25698 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 344 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 530 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 166 " distance=2.03 Simple disulfide: pdb=" SG CYS D 291 " - pdb=" SG CYS D 301 " distance=2.03 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 617 " - pdb=" SG CYS D 649 " distance=2.03 Simple disulfide: pdb=" SG CYS D 662 " - pdb=" SG CYS D 671 " distance=2.03 Simple disulfide: pdb=" SG CYS D 738 " - pdb=" SG CYS D 760 " distance=2.02 Simple disulfide: pdb=" SG CYS D 743 " - pdb=" SG CYS D 749 " distance=2.03 Simple disulfide: pdb=" SG CYS D1032 " - pdb=" SG CYS D1043 " distance=2.03 Simple disulfide: pdb=" SG CYS D1082 " - pdb=" SG CYS D1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.04 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.03 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1134 " " NAG B1311 " - " ASN B 165 " " NAG D1301 " - " ASN D 61 " " NAG D1302 " - " ASN D 122 " " NAG D1303 " - " ASN D 234 " " NAG D1304 " - " ASN D 282 " " NAG D1305 " - " ASN D 343 " " NAG D1306 " - " ASN D 616 " " NAG D1307 " - " ASN D 657 " " NAG D1308 " - " ASN D 709 " " NAG D1309 " - " ASN D1074 " " NAG D1310 " - " ASN D1134 " " NAG D1311 " - " ASN D 165 " " NAG F1301 " - " ASN F 61 " " NAG F1302 " - " ASN F 122 " " NAG F1303 " - " ASN F 234 " " NAG F1304 " - " ASN F 282 " " NAG F1305 " - " ASN F 343 " " NAG F1306 " - " ASN F 616 " " NAG F1307 " - " ASN F 657 " " NAG F1308 " - " ASN F 709 " " NAG F1309 " - " ASN F1074 " " NAG F1310 " - " ASN F1134 " " NAG F1311 " - " ASN F 165 " " NAG G 1 " - " ASN B 331 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN B 801 " " NAG J 1 " - " ASN B1098 " " NAG K 1 " - " ASN D 331 " " NAG L 1 " - " ASN D 717 " " NAG M 1 " - " ASN D 801 " " NAG N 1 " - " ASN D1098 " " NAG O 1 " - " ASN F 331 " " NAG P 1 " - " ASN F 717 " " NAG Q 1 " - " ASN F 801 " " NAG R 1 " - " ASN F1098 " Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 2.6 seconds 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9358 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 59 sheets defined 40.2% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid -28 through -20 Processing helix chain 'A' and resid -19 through -17 No H-bonds generated for 'chain 'A' and resid -19 through -17' Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.867A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 removed outlier: 3.622A pdb=" N MET A 62 " --> pdb=" O ASN A 58 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN A 63 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N MET A 82 " --> pdb=" O THR A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 101 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.702A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU A 108 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.780A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix removed outlier: 3.519A pdb=" N ALA A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 365 through 383 Processing helix chain 'A' and resid 400 through 414 removed outlier: 3.924A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 446 Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.528A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 534 removed outlier: 4.321A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.988A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.600A pdb=" N LEU A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 4.445A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 409 removed outlier: 3.632A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.779A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.810A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.161A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.660A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.628A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.634A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'C' and resid -28 through -20 Processing helix chain 'C' and resid 20 through 53 removed outlier: 3.648A pdb=" N ASP C 38 " --> pdb=" O HIS C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 82 removed outlier: 4.234A pdb=" N MET C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 101 Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.959A pdb=" N SER C 106 " --> pdb=" O ASN C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 130 Processing helix chain 'C' and resid 146 through 154 Processing helix chain 'C' and resid 157 through 194 removed outlier: 3.839A pdb=" N GLN C 175 " --> pdb=" O GLU C 171 " (cutoff:3.500A) Proline residue: C 178 - end of helix removed outlier: 3.564A pdb=" N ALA C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 205 Processing helix chain 'C' and resid 218 through 252 removed outlier: 3.738A pdb=" N LEU C 222 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE C 223 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Proline residue: C 235 - end of helix Processing helix chain 'C' and resid 265 through 268 removed outlier: 4.349A pdb=" N GLY C 268 " --> pdb=" O HIS C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'C' and resid 276 through 280 removed outlier: 3.834A pdb=" N SER C 280 " --> pdb=" O ASN C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 300 Processing helix chain 'C' and resid 303 through 318 Processing helix chain 'C' and resid 324 through 331 removed outlier: 4.295A pdb=" N TRP C 328 " --> pdb=" O THR C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 385 removed outlier: 3.888A pdb=" N TYR C 385 " --> pdb=" O TYR C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 414 removed outlier: 3.897A pdb=" N MET C 408 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER C 409 " --> pdb=" O GLY C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 448 through 466 removed outlier: 4.499A pdb=" N PHE C 452 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 472 through 484 Processing helix chain 'C' and resid 498 through 502 Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 512 through 534 removed outlier: 4.259A pdb=" N TYR C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 542 Processing helix chain 'C' and resid 547 through 559 removed outlier: 3.756A pdb=" N GLY C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET C 557 " --> pdb=" O LYS C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 574 Processing helix chain 'C' and resid 581 through 588 removed outlier: 3.698A pdb=" N LEU C 585 " --> pdb=" O VAL C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 588 through 599 Processing helix chain 'D' and resid 294 through 304 Processing helix chain 'D' and resid 338 through 343 Processing helix chain 'D' and resid 365 through 371 Processing helix chain 'D' and resid 383 through 389 removed outlier: 3.723A pdb=" N ASN D 388 " --> pdb=" O PRO D 384 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP D 389 " --> pdb=" O THR D 385 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 409 removed outlier: 3.577A pdb=" N VAL D 407 " --> pdb=" O GLY D 404 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 422 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 502 through 506 Processing helix chain 'D' and resid 737 through 742 Processing helix chain 'D' and resid 746 through 754 removed outlier: 3.691A pdb=" N SER D 750 " --> pdb=" O SER D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 758 through 783 removed outlier: 3.604A pdb=" N GLN D 762 " --> pdb=" O SER D 758 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 826 removed outlier: 3.558A pdb=" N VAL D 826 " --> pdb=" O LEU D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 885 Processing helix chain 'D' and resid 886 through 891 removed outlier: 4.077A pdb=" N GLY D 891 " --> pdb=" O PHE D 888 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 908 Processing helix chain 'D' and resid 913 through 918 Processing helix chain 'D' and resid 919 through 941 removed outlier: 3.547A pdb=" N GLN D 935 " --> pdb=" O ILE D 931 " (cutoff:3.500A) Processing helix chain 'D' and resid 945 through 965 removed outlier: 3.524A pdb=" N VAL D 951 " --> pdb=" O LYS D 947 " (cutoff:3.500A) Processing helix chain 'D' and resid 966 through 968 No H-bonds generated for 'chain 'D' and resid 966 through 968' Processing helix chain 'D' and resid 976 through 982 Processing helix chain 'D' and resid 985 through 1032 removed outlier: 4.374A pdb=" N VAL D 991 " --> pdb=" O PRO D 987 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY D 999 " --> pdb=" O ARG D 995 " (cutoff:3.500A) Processing helix chain 'E' and resid -28 through -20 Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.813A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 82 removed outlier: 3.512A pdb=" N MET E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 101 Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.602A pdb=" N LEU E 108 " --> pdb=" O SER E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 129 Processing helix chain 'E' and resid 146 through 155 Processing helix chain 'E' and resid 157 through 172 Processing helix chain 'E' and resid 172 through 194 Proline residue: E 178 - end of helix Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 218 through 252 removed outlier: 3.704A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 275 through 277 No H-bonds generated for 'chain 'E' and resid 275 through 277' Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 293 through 301 removed outlier: 3.631A pdb=" N MET E 297 " --> pdb=" O VAL E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 318 Processing helix chain 'E' and resid 325 through 331 Processing helix chain 'E' and resid 365 through 385 Processing helix chain 'E' and resid 386 through 388 No H-bonds generated for 'chain 'E' and resid 386 through 388' Processing helix chain 'E' and resid 400 through 413 Processing helix chain 'E' and resid 414 through 421 Processing helix chain 'E' and resid 431 through 446 Processing helix chain 'E' and resid 448 through 465 removed outlier: 4.208A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.686A pdb=" N GLU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG E 482 " --> pdb=" O TRP E 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 533 removed outlier: 4.324A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.522A pdb=" N GLY E 551 " --> pdb=" O SER E 547 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 574 removed outlier: 4.080A pdb=" N VAL E 573 " --> pdb=" O ALA E 569 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 588 Processing helix chain 'E' and resid 588 through 599 Processing helix chain 'F' and resid 294 through 304 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'F' and resid 385 through 390 Processing helix chain 'F' and resid 404 through 408 removed outlier: 3.690A pdb=" N VAL F 407 " --> pdb=" O GLY F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 422 Processing helix chain 'F' and resid 502 through 506 Processing helix chain 'F' and resid 616 through 620 removed outlier: 3.724A pdb=" N VAL F 620 " --> pdb=" O CYS F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 737 through 743 Processing helix chain 'F' and resid 746 through 755 Processing helix chain 'F' and resid 758 through 783 Processing helix chain 'F' and resid 816 through 826 Processing helix chain 'F' and resid 866 through 885 Processing helix chain 'F' and resid 886 through 891 removed outlier: 4.062A pdb=" N GLY F 891 " --> pdb=" O PHE F 888 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 909 Processing helix chain 'F' and resid 913 through 918 Processing helix chain 'F' and resid 919 through 941 removed outlier: 3.528A pdb=" N GLN F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) Processing helix chain 'F' and resid 945 through 965 removed outlier: 3.592A pdb=" N GLN F 949 " --> pdb=" O LEU F 945 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N VAL F 951 " --> pdb=" O LYS F 947 " (cutoff:3.500A) Processing helix chain 'F' and resid 966 through 968 No H-bonds generated for 'chain 'F' and resid 966 through 968' Processing helix chain 'F' and resid 976 through 982 Processing helix chain 'F' and resid 985 through 1032 removed outlier: 4.462A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid -36 through -35 removed outlier: 3.901A pdb=" N TRP E -30 " --> pdb=" O PHE E -10 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU E -3 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE E 5 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ARG C 13 " --> pdb=" O PHE E 5 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LYS E 7 " --> pdb=" O GLU C 11 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid -36 through -35 removed outlier: 4.545A pdb=" N LEU A -3 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N PHE A 5 " --> pdb=" O ARG E 13 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ARG E 13 " --> pdb=" O PHE A 5 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N LYS A 7 " --> pdb=" O GLU E 11 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 14 removed outlier: 5.035A pdb=" N LYS C 7 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ARG A 13 " --> pdb=" O PHE C 5 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE C 5 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU C -3 " --> pdb=" O VAL C 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.604A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 347 through 352 removed outlier: 3.595A pdb=" N THR A 347 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 28 through 30 removed outlier: 7.887A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.716A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.912A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.502A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.237A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 325 through 328 Processing sheet with id=AB5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AB6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AB7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB8, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.907A pdb=" N PHE B 565 " --> pdb=" O PHE F 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.946A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.870A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.233A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.772A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1094 through 1097 removed outlier: 4.775A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 131 through 133 Processing sheet with id=AC6, first strand: chain 'C' and resid 262 through 263 removed outlier: 5.381A pdb=" N LEU C 262 " --> pdb=" O VAL C 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 347 through 352 removed outlier: 6.342A pdb=" N ASP C 355 " --> pdb=" O LEU C 351 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 28 through 30 removed outlier: 8.081A pdb=" N ASN D 61 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N TYR D 269 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N SER D 205 " --> pdb=" O PRO D 225 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 42 through 43 removed outlier: 4.212A pdb=" N ALA F 575 " --> pdb=" O GLY F 566 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASP F 574 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F 543 " --> pdb=" O LEU F 546 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL F 539 " --> pdb=" O GLY F 550 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLU F 324 " --> pdb=" O ASN F 540 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ASN F 542 " --> pdb=" O GLU F 324 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE F 326 " --> pdb=" O ASN F 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.959A pdb=" N ASP D 287 " --> pdb=" O LYS D 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 84 through 85 removed outlier: 5.523A pdb=" N LEU D 141 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 84 through 85 Processing sheet with id=AD4, first strand: chain 'D' and resid 311 through 319 removed outlier: 5.153A pdb=" N ILE D 312 " --> pdb=" O THR D 599 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N THR D 599 " --> pdb=" O ILE D 312 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN D 314 " --> pdb=" O VAL D 597 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL D 597 " --> pdb=" O GLN D 314 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER D 316 " --> pdb=" O VAL D 595 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLY D 594 " --> pdb=" O GLN D 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 325 through 328 Processing sheet with id=AD6, first strand: chain 'D' and resid 354 through 358 Processing sheet with id=AD7, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AD8, first strand: chain 'D' and resid 473 through 474 Processing sheet with id=AD9, first strand: chain 'D' and resid 654 through 655 removed outlier: 6.493A pdb=" N ILE D 670 " --> pdb=" O ILE D 666 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 711 through 728 removed outlier: 6.877A pdb=" N SER D 711 " --> pdb=" O THR D1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR D1076 " --> pdb=" O SER D 711 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA D 713 " --> pdb=" O ASN D1074 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN D1074 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLU D1072 " --> pdb=" O PRO D 715 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1047 through 1050 removed outlier: 6.797A pdb=" N VAL D1065 " --> pdb=" O LEU D1049 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA D1078 " --> pdb=" O PHE D1095 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE D1095 " --> pdb=" O ALA D1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 733 through 736 removed outlier: 4.342A pdb=" N LYS D 733 " --> pdb=" O LEU D 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1120 through 1125 removed outlier: 4.337A pdb=" N ALA D1087 " --> pdb=" O SER D1123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 131 through 133 Processing sheet with id=AE6, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.769A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 347 through 352 removed outlier: 5.746A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 29 through 30 removed outlier: 7.684A pdb=" N ASN F 61 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N TYR F 269 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ALA F 264 " --> pdb=" O THR F 95 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR F 95 " --> pdb=" O ALA F 264 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N SER F 205 " --> pdb=" O PRO F 225 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 47 through 55 removed outlier: 3.816A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 84 through 85 removed outlier: 6.309A pdb=" N ALA F 243 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE F 101 " --> pdb=" O ALA F 243 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 84 through 85 removed outlier: 5.640A pdb=" N LEU F 141 " --> pdb=" O LEU F 244 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 128 through 129 Processing sheet with id=AF4, first strand: chain 'F' and resid 311 through 319 removed outlier: 5.497A pdb=" N ILE F 312 " --> pdb=" O THR F 599 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR F 599 " --> pdb=" O ILE F 312 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N GLN F 314 " --> pdb=" O VAL F 597 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL F 597 " --> pdb=" O GLN F 314 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER F 316 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY F 594 " --> pdb=" O GLN F 613 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.517A pdb=" N LEU F 513 " --> pdb=" O CYS F 432 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 448 through 454 removed outlier: 5.886A pdb=" N TYR F 449 " --> pdb=" O PHE F 497 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N PHE F 497 " --> pdb=" O TYR F 449 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N TYR F 451 " --> pdb=" O TYR F 495 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AF8, first strand: chain 'F' and resid 653 through 655 removed outlier: 6.426A pdb=" N ALA F 672 " --> pdb=" O PRO F 665 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 711 through 715 Processing sheet with id=AG1, first strand: chain 'F' and resid 718 through 728 removed outlier: 6.800A pdb=" N VAL F1065 " --> pdb=" O LEU F1049 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 718 through 728 Processing sheet with id=AG3, first strand: chain 'F' and resid 733 through 736 removed outlier: 4.359A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 1120 through 1125 removed outlier: 4.277A pdb=" N ALA F1087 " --> pdb=" O SER F1123 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 1094 through 1096 1887 hydrogen bonds defined for protein. 5303 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: 11.18 Time building geometry restraints manager: 5.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12759 1.34 - 1.46: 8638 1.46 - 1.58: 19582 1.58 - 1.70: 0 1.70 - 1.82: 281 Bond restraints: 41260 Sorted by residual: bond pdb=" N VAL D 83 " pdb=" CA VAL D 83 " ideal model delta sigma weight residual 1.458 1.494 -0.035 1.21e-02 6.83e+03 8.49e+00 bond pdb=" N VAL D 90 " pdb=" CA VAL D 90 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.18e-02 7.18e+03 7.84e+00 bond pdb=" N THR E 365 " pdb=" CA THR E 365 " ideal model delta sigma weight residual 1.454 1.485 -0.032 1.18e-02 7.18e+03 7.20e+00 bond pdb=" N VAL E 364 " pdb=" CA VAL E 364 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.07e+00 bond pdb=" N ASP D 88 " pdb=" CA ASP D 88 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.85e+00 ... (remaining 41255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 55569 2.30 - 4.60: 487 4.60 - 6.91: 67 6.91 - 9.21: 15 9.21 - 11.51: 5 Bond angle restraints: 56143 Sorted by residual: angle pdb=" CA GLN E 472 " pdb=" CB GLN E 472 " pdb=" CG GLN E 472 " ideal model delta sigma weight residual 114.10 121.83 -7.73 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CB MET A 557 " pdb=" CG MET A 557 " pdb=" SD MET A 557 " ideal model delta sigma weight residual 112.70 124.21 -11.51 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C1 NAG F1310 " pdb=" O5 NAG F1310 " pdb=" C5 NAG F1310 " ideal model delta sigma weight residual 113.21 123.07 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C2 NAG J 2 " pdb=" N2 NAG J 2 " pdb=" C7 NAG J 2 " ideal model delta sigma weight residual 124.56 134.14 -9.58 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C2 NAG N 2 " pdb=" N2 NAG N 2 " pdb=" C7 NAG N 2 " ideal model delta sigma weight residual 124.56 134.05 -9.49 3.00e+00 1.11e-01 1.00e+01 ... (remaining 56138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 23090 21.26 - 42.52: 1753 42.52 - 63.77: 289 63.77 - 85.03: 107 85.03 - 106.29: 22 Dihedral angle restraints: 25261 sinusoidal: 10721 harmonic: 14540 Sorted by residual: dihedral pdb=" CB CYS F 743 " pdb=" SG CYS F 743 " pdb=" SG CYS F 749 " pdb=" CB CYS F 749 " ideal model delta sinusoidal sigma weight residual 93.00 -179.97 -87.03 1 1.00e+01 1.00e-02 9.10e+01 dihedral pdb=" CB CYS F 738 " pdb=" SG CYS F 738 " pdb=" SG CYS F 760 " pdb=" CB CYS F 760 " ideal model delta sinusoidal sigma weight residual -86.00 -3.25 -82.75 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 14.13 78.87 1 1.00e+01 1.00e-02 7.75e+01 ... (remaining 25258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 5755 0.073 - 0.147: 578 0.147 - 0.220: 19 0.220 - 0.293: 5 0.293 - 0.366: 3 Chirality restraints: 6360 Sorted by residual: chirality pdb=" C1 NAG D1311 " pdb=" ND2 ASN D 165 " pdb=" C2 NAG D1311 " pdb=" O5 NAG D1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" C1 NAG F1308 " pdb=" ND2 ASN F 709 " pdb=" C2 NAG F1308 " pdb=" O5 NAG F1308 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.19e+00 chirality pdb=" C1 NAG F1311 " pdb=" ND2 ASN F 165 " pdb=" C2 NAG F1311 " pdb=" O5 NAG F1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 6357 not shown) Planarity restraints: 7244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 165 " 0.021 2.00e-02 2.50e+03 2.00e-02 5.02e+00 pdb=" CG ASN D 165 " -0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN D 165 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN D 165 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG D1311 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 145 " -0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO C 146 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 414 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.80e+00 pdb=" N PRO C 415 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 415 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 415 " -0.023 5.00e-02 4.00e+02 ... (remaining 7241 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 428 2.56 - 3.14: 33098 3.14 - 3.73: 69343 3.73 - 4.31: 92165 4.31 - 4.90: 150090 Nonbonded interactions: 345124 Sorted by model distance: nonbonded pdb=" O LYS B 947 " pdb=" OD1 ASP B 950 " model vdw 1.970 3.040 nonbonded pdb=" OG1 THR F 618 " pdb=" OE1 GLU F 619 " model vdw 2.171 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.194 3.040 nonbonded pdb=" OG SER A 109 " pdb=" OD1 ASP A 111 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR E 217 " pdb=" OD2 ASP E 225 " model vdw 2.196 3.040 ... (remaining 345119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid -37 or resid -35 through -13 or resid -11 through -10 or r \ esid -8 or resid -6 through 8 or resid 10 through 12 or resid 14 through 19 or ( \ resid 20 and (name N or name CA or name C or name O or name CB )) or resid 21 th \ rough 614)) selection = (chain 'C' and (resid -37 or resid -35 through -13 or resid -11 through -10 or r \ esid -8 or resid -6 through 8 or resid 10 through 12 or resid 14 through 19 or ( \ resid 20 and (name N or name CA or name C or name O or name CB )) or resid 21 th \ rough 614)) selection = (chain 'E' and (resid -37 or resid -35 through -13 or resid -11 through -10 or r \ esid -8 or resid -6 through 8 or resid 10 through 12 or resid 14 through 479 or \ (resid 480 and (name N or name CA or name C or name O or name CB )) or resid 481 \ through 614)) } ncs_group { reference = (chain 'B' and (resid 27 through 520 or (resid 521 through 522 and (name N or na \ me CA or name C or name O or name CB )) or resid 523 through 579 or (resid 580 a \ nd (name N or name CA or name C or name O or name CB )) or resid 581 through 911 \ or (resid 912 and (name N or name CA or name C or name O or name CB )) or resid \ 913 through 1311)) selection = (chain 'D' and (resid 27 through 520 or (resid 521 through 522 and (name N or na \ me CA or name C or name O or name CB )) or resid 523 through 579 or (resid 580 a \ nd (name N or name CA or name C or name O or name CB )) or resid 581 through 911 \ or (resid 912 and (name N or name CA or name C or name O or name CB )) or resid \ 913 through 1311)) selection = (chain 'F' and (resid 27 through 214 or (resid 215 and (name N or name CA or nam \ e C or name O or name CB )) or resid 216 through 280 or (resid 281 and (name N o \ r name CA or name C or name O or name CB )) or resid 282 through 407 or (resid 4 \ 08 and (name N or name CA or name C or name O or name CB )) or resid 409 through \ 442 or (resid 443 and (name N or name CA or name C or name O or name CB )) or r \ esid 444 through 710 or (resid 711 and (name N or name CA or name C or name O or \ name CB )) or resid 712 through 1040 or (resid 1041 and (name N or name CA or n \ ame C or name O or name CB )) or resid 1042 through 1099 or (resid 1100 and (nam \ e N or name CA or name C or name O or name CB )) or resid 1101 through 1126 or ( \ resid 1127 and (name N or name CA or name C or name O or name CB )) or resid 112 \ 8 through 1311)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.780 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.920 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 47.500 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.150 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41362 Z= 0.162 Angle : 0.563 11.511 56404 Z= 0.274 Chirality : 0.042 0.366 6360 Planarity : 0.003 0.042 7199 Dihedral : 15.567 106.291 15768 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.31 % Allowed : 11.34 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.12), residues: 4928 helix: 1.65 (0.13), residues: 1802 sheet: -0.41 (0.18), residues: 833 loop : -0.41 (0.13), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 815 TYR 0.013 0.001 TYR B1067 PHE 0.014 0.001 PHE B 464 TRP 0.011 0.001 TRP B 104 HIS 0.005 0.001 HIS C 373 Details of bonding type rmsd covalent geometry : bond 0.00347 (41260) covalent geometry : angle 0.54047 (56143) SS BOND : bond 0.00219 ( 45) SS BOND : angle 0.95251 ( 90) hydrogen bonds : bond 0.19794 ( 1873) hydrogen bonds : angle 7.32993 ( 5303) link_BETA1-4 : bond 0.00837 ( 12) link_BETA1-4 : angle 3.21092 ( 36) link_NAG-ASN : bond 0.00408 ( 45) link_NAG-ASN : angle 2.73249 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 127 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 499 ASP cc_start: -0.0008 (OUTLIER) cc_final: -0.0584 (m-30) REVERT: A 600 LYS cc_start: 0.7805 (OUTLIER) cc_final: 0.7583 (tppt) REVERT: B 1122 VAL cc_start: 0.9614 (OUTLIER) cc_final: 0.9345 (t) REVERT: B 1142 GLN cc_start: 0.9110 (mm110) cc_final: 0.8523 (mm-40) REVERT: E 383 MET cc_start: 0.6486 (mtp) cc_final: 0.5757 (ttm) REVERT: E 600 LYS cc_start: 0.6805 (OUTLIER) cc_final: 0.6586 (mmtp) REVERT: F 725 GLU cc_start: 0.9040 (tp30) cc_final: 0.8727 (tt0) outliers start: 53 outliers final: 42 residues processed: 175 average time/residue: 0.2344 time to fit residues: 72.9179 Evaluate side-chains 172 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 126 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain F residue 87 ASN Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 723 THR Chi-restraints excluded: chain F residue 749 CYS Chi-restraints excluded: chain F residue 754 LEU Chi-restraints excluded: chain F residue 916 LEU Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1128 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 50.0000 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 0.4980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 30.0000 chunk 132 optimal weight: 4.9990 chunk 494 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.0570 overall best weight: 2.1104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN A 89 GLN A 250 ASN A 330 ASN ** B1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C -6 GLN ** D 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.111875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.067136 restraints weight = 394908.816| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 9.20 r_work: 0.2838 rms_B_bonded: 6.15 restraints_weight: 2.0000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 41362 Z= 0.148 Angle : 0.586 10.151 56404 Z= 0.288 Chirality : 0.044 0.378 6360 Planarity : 0.004 0.041 7199 Dihedral : 8.883 105.360 6621 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.95 % Allowed : 10.90 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.12), residues: 4928 helix: 1.85 (0.12), residues: 1780 sheet: -0.51 (0.18), residues: 791 loop : -0.37 (0.13), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 219 TYR 0.021 0.001 TYR B1067 PHE 0.012 0.001 PHE E 369 TRP 0.018 0.001 TRP E 163 HIS 0.006 0.001 HIS A 401 Details of bonding type rmsd covalent geometry : bond 0.00319 (41260) covalent geometry : angle 0.56420 (56143) SS BOND : bond 0.00292 ( 45) SS BOND : angle 1.22474 ( 90) hydrogen bonds : bond 0.04498 ( 1873) hydrogen bonds : angle 5.46343 ( 5303) link_BETA1-4 : bond 0.00866 ( 12) link_BETA1-4 : angle 3.22458 ( 36) link_NAG-ASN : bond 0.00427 ( 45) link_NAG-ASN : angle 2.73261 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 130 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 600 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7389 (tppt) REVERT: B 365 TYR cc_start: 0.9451 (m-80) cc_final: 0.9158 (m-80) REVERT: D 568 ASP cc_start: 0.9064 (t0) cc_final: 0.8805 (t0) REVERT: E 366 MET cc_start: 0.7997 (tpp) cc_final: 0.7764 (ttm) REVERT: E 383 MET cc_start: 0.6323 (mtp) cc_final: 0.5276 (ttm) REVERT: E 600 LYS cc_start: 0.6657 (OUTLIER) cc_final: 0.6436 (mptt) outliers start: 81 outliers final: 49 residues processed: 203 average time/residue: 0.2155 time to fit residues: 77.8521 Evaluate side-chains 177 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 763 LEU Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 363 LYS Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 551 VAL Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 749 CYS Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 462 optimal weight: 7.9990 chunk 367 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 244 optimal weight: 0.0670 chunk 474 optimal weight: 0.9990 chunk 390 optimal weight: 8.9990 chunk 477 optimal weight: 3.9990 chunk 429 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 156 optimal weight: 0.5980 overall best weight: 1.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN A 103 ASN A 250 ASN A 556 ASN B 239 GLN B 751 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN C 49 ASN D 501 ASN ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 751 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.112449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.068940 restraints weight = 358191.636| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 7.47 r_work: 0.2888 rms_B_bonded: 5.79 restraints_weight: 2.0000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 41362 Z= 0.114 Angle : 0.559 10.866 56404 Z= 0.270 Chirality : 0.043 0.362 6360 Planarity : 0.003 0.044 7199 Dihedral : 8.610 104.770 6589 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.89 % Allowed : 11.66 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.12), residues: 4928 helix: 1.81 (0.12), residues: 1789 sheet: -0.45 (0.18), residues: 789 loop : -0.36 (0.13), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 460 TYR 0.020 0.001 TYR B1067 PHE 0.011 0.001 PHE A 369 TRP 0.017 0.001 TRP E 163 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00242 (41260) covalent geometry : angle 0.53769 (56143) SS BOND : bond 0.00246 ( 45) SS BOND : angle 0.97014 ( 90) hydrogen bonds : bond 0.03962 ( 1873) hydrogen bonds : angle 5.13069 ( 5303) link_BETA1-4 : bond 0.00962 ( 12) link_BETA1-4 : angle 3.22006 ( 36) link_NAG-ASN : bond 0.00423 ( 45) link_NAG-ASN : angle 2.61661 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 136 time to evaluate : 1.719 Fit side-chains revert: symmetry clash REVERT: A 600 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7115 (tppt) REVERT: B 84 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8510 (mm) REVERT: B 365 TYR cc_start: 0.9411 (m-80) cc_final: 0.9187 (m-80) REVERT: B 955 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.8894 (t0) REVERT: B 1142 GLN cc_start: 0.9127 (mm110) cc_final: 0.8520 (mm-40) REVERT: C 463 VAL cc_start: 0.3756 (OUTLIER) cc_final: 0.3360 (p) REVERT: D 762 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.8840 (pm20) REVERT: D 779 GLN cc_start: 0.9417 (tm-30) cc_final: 0.9128 (tm-30) REVERT: E 152 MET cc_start: -0.1106 (mtp) cc_final: -0.1385 (mtp) REVERT: E 383 MET cc_start: 0.5655 (mtp) cc_final: 0.4381 (ttm) REVERT: E 600 LYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6548 (mptt) REVERT: E 610 TRP cc_start: 0.8136 (t60) cc_final: 0.7859 (t60) REVERT: F 725 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: F 1019 ARG cc_start: 0.9337 (tpt170) cc_final: 0.8910 (tpt170) outliers start: 78 outliers final: 48 residues processed: 207 average time/residue: 0.2147 time to fit residues: 79.3653 Evaluate side-chains 186 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 131 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 762 GLN Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain E residue 600 LYS Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 551 VAL Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 725 GLU Chi-restraints excluded: chain F residue 749 CYS Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 916 LEU Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1128 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 58 optimal weight: 20.0000 chunk 306 optimal weight: 0.8980 chunk 373 optimal weight: 50.0000 chunk 422 optimal weight: 0.0020 chunk 90 optimal weight: 0.0060 chunk 459 optimal weight: 0.8980 chunk 134 optimal weight: 8.9990 chunk 298 optimal weight: 0.6980 chunk 412 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 421 optimal weight: 50.0000 overall best weight: 0.5004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.112872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.069116 restraints weight = 428966.955| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 10.20 r_work: 0.2886 rms_B_bonded: 6.46 restraints_weight: 2.0000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 41362 Z= 0.100 Angle : 0.548 10.350 56404 Z= 0.264 Chirality : 0.043 0.355 6360 Planarity : 0.003 0.044 7199 Dihedral : 8.398 103.012 6579 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.00 % Allowed : 12.01 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.12), residues: 4928 helix: 1.89 (0.12), residues: 1780 sheet: -0.32 (0.18), residues: 799 loop : -0.31 (0.13), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.021 0.001 TYR B1067 PHE 0.013 0.001 PHE B 456 TRP 0.015 0.001 TRP E 163 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00209 (41260) covalent geometry : angle 0.52634 (56143) SS BOND : bond 0.00294 ( 45) SS BOND : angle 1.33752 ( 90) hydrogen bonds : bond 0.03578 ( 1873) hydrogen bonds : angle 4.92002 ( 5303) link_BETA1-4 : bond 0.01012 ( 12) link_BETA1-4 : angle 3.21700 ( 36) link_NAG-ASN : bond 0.00442 ( 45) link_NAG-ASN : angle 2.53593 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 144 time to evaluate : 1.635 Fit side-chains revert: symmetry clash REVERT: A 600 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7443 (tppt) REVERT: B 84 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8455 (mm) REVERT: B 365 TYR cc_start: 0.9388 (m-80) cc_final: 0.9142 (m-80) REVERT: B 864 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8856 (mp) REVERT: B 955 ASN cc_start: 0.9338 (OUTLIER) cc_final: 0.8944 (t0) REVERT: B 1142 GLN cc_start: 0.9135 (mm110) cc_final: 0.8548 (mm-40) REVERT: D 568 ASP cc_start: 0.9060 (t0) cc_final: 0.8832 (t0) REVERT: D 762 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.8830 (pm20) REVERT: D 779 GLN cc_start: 0.9358 (tm-30) cc_final: 0.9090 (tm-30) REVERT: E 383 MET cc_start: 0.5928 (mtp) cc_final: 0.5107 (ttm) REVERT: F 725 GLU cc_start: 0.9033 (tp30) cc_final: 0.8626 (tt0) REVERT: F 1019 ARG cc_start: 0.9397 (tpt170) cc_final: 0.8992 (tpt170) REVERT: F 1113 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8814 (pm20) outliers start: 83 outliers final: 54 residues processed: 223 average time/residue: 0.2163 time to fit residues: 85.4895 Evaluate side-chains 196 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 136 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 762 GLN Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 551 VAL Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 749 CYS Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 916 LEU Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1128 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 180 optimal weight: 10.0000 chunk 442 optimal weight: 0.0670 chunk 118 optimal weight: 0.9990 chunk 483 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 344 optimal weight: 50.0000 chunk 199 optimal weight: 40.0000 chunk 339 optimal weight: 8.9990 chunk 185 optimal weight: 50.0000 chunk 491 optimal weight: 7.9990 chunk 476 optimal weight: 0.8980 overall best weight: 1.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1010 GLN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.112265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.067732 restraints weight = 377776.437| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 8.41 r_work: 0.2879 rms_B_bonded: 6.10 restraints_weight: 2.0000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 41362 Z= 0.133 Angle : 0.557 10.955 56404 Z= 0.267 Chirality : 0.042 0.360 6360 Planarity : 0.003 0.043 7199 Dihedral : 8.251 102.787 6573 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.21 % Allowed : 11.94 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.12), residues: 4928 helix: 1.94 (0.12), residues: 1786 sheet: -0.38 (0.18), residues: 824 loop : -0.28 (0.13), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 192 TYR 0.020 0.001 TYR B1067 PHE 0.011 0.001 PHE B 92 TRP 0.015 0.001 TRP E 163 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00294 (41260) covalent geometry : angle 0.53627 (56143) SS BOND : bond 0.00237 ( 45) SS BOND : angle 1.19241 ( 90) hydrogen bonds : bond 0.03553 ( 1873) hydrogen bonds : angle 4.89405 ( 5303) link_BETA1-4 : bond 0.00907 ( 12) link_BETA1-4 : angle 3.21535 ( 36) link_NAG-ASN : bond 0.00393 ( 45) link_NAG-ASN : angle 2.54713 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 134 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: A 579 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.5647 (mpp) REVERT: A 600 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7350 (tppt) REVERT: B 84 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8404 (mm) REVERT: B 365 TYR cc_start: 0.9397 (m-80) cc_final: 0.9179 (m-80) REVERT: B 955 ASN cc_start: 0.9323 (OUTLIER) cc_final: 0.8912 (t0) REVERT: B 1142 GLN cc_start: 0.9133 (mm110) cc_final: 0.8517 (mm-40) REVERT: D 568 ASP cc_start: 0.9039 (t0) cc_final: 0.8805 (t0) REVERT: D 762 GLN cc_start: 0.9312 (OUTLIER) cc_final: 0.8782 (pm20) REVERT: D 779 GLN cc_start: 0.9374 (tm-30) cc_final: 0.9124 (tm-30) REVERT: D 909 ILE cc_start: 0.9648 (OUTLIER) cc_final: 0.9401 (tp) REVERT: E 383 MET cc_start: 0.5998 (mtp) cc_final: 0.5147 (ttm) REVERT: F 725 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8623 (tt0) REVERT: F 909 ILE cc_start: 0.9541 (OUTLIER) cc_final: 0.9307 (tp) REVERT: F 1113 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8840 (pm20) outliers start: 92 outliers final: 65 residues processed: 216 average time/residue: 0.2256 time to fit residues: 87.0873 Evaluate side-chains 207 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 133 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 762 GLN Chi-restraints excluded: chain D residue 869 MET Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 916 LEU Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1096 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 365 THR Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 551 VAL Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 725 GLU Chi-restraints excluded: chain F residue 749 CYS Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 909 ILE Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 916 LEU Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1128 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 174 optimal weight: 7.9990 chunk 455 optimal weight: 0.9990 chunk 422 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 341 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 316 optimal weight: 0.9990 chunk 47 optimal weight: 8.9990 chunk 405 optimal weight: 0.0070 chunk 414 optimal weight: 0.4980 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.112921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.069773 restraints weight = 394046.886| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 8.95 r_work: 0.2889 rms_B_bonded: 6.37 restraints_weight: 2.0000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 41362 Z= 0.100 Angle : 0.555 12.181 56404 Z= 0.264 Chirality : 0.042 0.351 6360 Planarity : 0.003 0.043 7199 Dihedral : 8.050 101.814 6571 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.95 % Allowed : 12.33 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.12), residues: 4928 helix: 1.94 (0.12), residues: 1791 sheet: -0.28 (0.18), residues: 830 loop : -0.28 (0.13), residues: 2307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 319 TYR 0.020 0.001 TYR B1067 PHE 0.017 0.001 PHE C 315 TRP 0.014 0.001 TRP E 163 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00209 (41260) covalent geometry : angle 0.53476 (56143) SS BOND : bond 0.00233 ( 45) SS BOND : angle 0.94991 ( 90) hydrogen bonds : bond 0.03426 ( 1873) hydrogen bonds : angle 4.78393 ( 5303) link_BETA1-4 : bond 0.01003 ( 12) link_BETA1-4 : angle 3.21856 ( 36) link_NAG-ASN : bond 0.00459 ( 45) link_NAG-ASN : angle 2.51454 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 137 time to evaluate : 1.612 Fit side-chains revert: symmetry clash REVERT: A 579 MET cc_start: 0.6953 (OUTLIER) cc_final: 0.4606 (mpp) REVERT: A 600 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7074 (tppt) REVERT: B 84 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8381 (mm) REVERT: B 365 TYR cc_start: 0.9360 (m-80) cc_final: 0.9132 (m-80) REVERT: B 955 ASN cc_start: 0.9322 (OUTLIER) cc_final: 0.8911 (t0) REVERT: B 1142 GLN cc_start: 0.9125 (mm110) cc_final: 0.8511 (mm-40) REVERT: C -1 VAL cc_start: 0.6923 (OUTLIER) cc_final: 0.6656 (m) REVERT: D 53 ASP cc_start: 0.9033 (t0) cc_final: 0.8810 (t0) REVERT: D 568 ASP cc_start: 0.9059 (t0) cc_final: 0.8832 (t0) REVERT: D 762 GLN cc_start: 0.9309 (OUTLIER) cc_final: 0.8842 (pm20) REVERT: D 779 GLN cc_start: 0.9363 (tm-30) cc_final: 0.8915 (tm-30) REVERT: E 152 MET cc_start: -0.0670 (mtp) cc_final: -0.0912 (mtp) REVERT: E 383 MET cc_start: 0.5897 (mtp) cc_final: 0.4902 (ttm) REVERT: F 725 GLU cc_start: 0.8989 (tp30) cc_final: 0.8670 (tt0) REVERT: F 909 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9289 (tp) REVERT: F 1113 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8831 (pm20) outliers start: 81 outliers final: 54 residues processed: 210 average time/residue: 0.2111 time to fit residues: 80.2114 Evaluate side-chains 193 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 131 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue -1 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 130 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 394 ASN Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 762 GLN Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 551 VAL Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 749 CYS Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 909 ILE Chi-restraints excluded: chain F residue 916 LEU Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1128 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 146 optimal weight: 8.9990 chunk 64 optimal weight: 0.0670 chunk 215 optimal weight: 9.9990 chunk 165 optimal weight: 50.0000 chunk 277 optimal weight: 4.9990 chunk 448 optimal weight: 6.9990 chunk 462 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 254 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 394 ASN ** E 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.111057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.065767 restraints weight = 346004.966| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 9.41 r_work: 0.2823 rms_B_bonded: 5.93 restraints_weight: 2.0000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 41362 Z= 0.214 Angle : 0.604 11.605 56404 Z= 0.290 Chirality : 0.043 0.375 6360 Planarity : 0.003 0.043 7199 Dihedral : 8.048 103.623 6570 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.09 % Allowed : 12.51 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.12), residues: 4928 helix: 1.91 (0.12), residues: 1802 sheet: -0.42 (0.18), residues: 810 loop : -0.30 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 815 TYR 0.020 0.001 TYR B1067 PHE 0.014 0.001 PHE D 898 TRP 0.014 0.001 TRP E 163 HIS 0.004 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00481 (41260) covalent geometry : angle 0.58253 (56143) SS BOND : bond 0.00283 ( 45) SS BOND : angle 1.18281 ( 90) hydrogen bonds : bond 0.03633 ( 1873) hydrogen bonds : angle 4.91068 ( 5303) link_BETA1-4 : bond 0.00821 ( 12) link_BETA1-4 : angle 3.22727 ( 36) link_NAG-ASN : bond 0.00417 ( 45) link_NAG-ASN : angle 2.74990 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 129 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.5558 (mtm) REVERT: A 600 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7130 (tppt) REVERT: B 84 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8460 (mm) REVERT: B 365 TYR cc_start: 0.9405 (m-80) cc_final: 0.9157 (m-80) REVERT: B 955 ASN cc_start: 0.9349 (OUTLIER) cc_final: 0.8922 (t0) REVERT: B 1092 GLU cc_start: 0.9289 (pm20) cc_final: 0.8933 (pm20) REVERT: B 1142 GLN cc_start: 0.9174 (mm110) cc_final: 0.8548 (mm-40) REVERT: C -1 VAL cc_start: 0.6827 (OUTLIER) cc_final: 0.6560 (m) REVERT: D 53 ASP cc_start: 0.9051 (t0) cc_final: 0.8804 (t0) REVERT: D 495 TYR cc_start: 0.5278 (OUTLIER) cc_final: 0.3630 (m-10) REVERT: D 568 ASP cc_start: 0.9092 (t0) cc_final: 0.8837 (t0) REVERT: D 762 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.8789 (pm20) REVERT: D 909 ILE cc_start: 0.9668 (OUTLIER) cc_final: 0.9422 (tp) REVERT: E 152 MET cc_start: -0.1690 (mtp) cc_final: -0.1936 (mtp) REVERT: E 383 MET cc_start: 0.5826 (mtp) cc_final: 0.4835 (ttm) REVERT: F 725 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8759 (tt0) REVERT: F 909 ILE cc_start: 0.9560 (OUTLIER) cc_final: 0.9312 (tp) outliers start: 87 outliers final: 67 residues processed: 206 average time/residue: 0.2127 time to fit residues: 78.8114 Evaluate side-chains 204 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 127 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue -1 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 762 GLN Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 551 VAL Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 725 GLU Chi-restraints excluded: chain F residue 749 CYS Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 909 ILE Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 916 LEU Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1128 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 344 optimal weight: 50.0000 chunk 388 optimal weight: 0.1980 chunk 145 optimal weight: 4.9990 chunk 191 optimal weight: 10.0000 chunk 318 optimal weight: 0.9980 chunk 17 optimal weight: 50.0000 chunk 411 optimal weight: 1.9990 chunk 228 optimal weight: 20.0000 chunk 6 optimal weight: 30.0000 chunk 284 optimal weight: 3.9990 chunk 73 optimal weight: 20.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 601 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 GLN ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.111606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.065741 restraints weight = 428821.602| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 10.14 r_work: 0.2832 rms_B_bonded: 6.62 restraints_weight: 2.0000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2780 r_free = 0.2780 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2780 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41362 Z= 0.149 Angle : 0.573 11.723 56404 Z= 0.274 Chirality : 0.043 0.360 6360 Planarity : 0.003 0.043 7199 Dihedral : 7.923 103.360 6570 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.98 % Allowed : 12.67 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 4928 helix: 1.94 (0.12), residues: 1791 sheet: -0.44 (0.17), residues: 820 loop : -0.28 (0.13), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.020 0.001 TYR B1067 PHE 0.014 0.001 PHE D 898 TRP 0.013 0.001 TRP E 163 HIS 0.004 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00332 (41260) covalent geometry : angle 0.55135 (56143) SS BOND : bond 0.00254 ( 45) SS BOND : angle 1.06825 ( 90) hydrogen bonds : bond 0.03477 ( 1873) hydrogen bonds : angle 4.83642 ( 5303) link_BETA1-4 : bond 0.00909 ( 12) link_BETA1-4 : angle 3.19940 ( 36) link_NAG-ASN : bond 0.00382 ( 45) link_NAG-ASN : angle 2.68456 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 126 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6327 (mtm) REVERT: A 600 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7399 (tppt) REVERT: B 84 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8450 (mm) REVERT: B 104 TRP cc_start: 0.7829 (OUTLIER) cc_final: 0.6877 (t-100) REVERT: B 365 TYR cc_start: 0.9406 (m-80) cc_final: 0.9151 (m-80) REVERT: B 955 ASN cc_start: 0.9345 (OUTLIER) cc_final: 0.8933 (t0) REVERT: C -1 VAL cc_start: 0.6942 (OUTLIER) cc_final: 0.6706 (m) REVERT: D 53 ASP cc_start: 0.9021 (t0) cc_final: 0.8779 (t0) REVERT: D 495 TYR cc_start: 0.4737 (OUTLIER) cc_final: 0.3429 (m-10) REVERT: D 568 ASP cc_start: 0.9093 (t0) cc_final: 0.8840 (t0) REVERT: D 762 GLN cc_start: 0.9333 (OUTLIER) cc_final: 0.8803 (pm20) REVERT: E 383 MET cc_start: 0.6124 (mtp) cc_final: 0.5387 (ttm) REVERT: F 725 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8755 (tt0) REVERT: F 909 ILE cc_start: 0.9525 (OUTLIER) cc_final: 0.9303 (tp) outliers start: 82 outliers final: 66 residues processed: 200 average time/residue: 0.2018 time to fit residues: 73.1079 Evaluate side-chains 201 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 125 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain A residue 601 ASN Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue -1 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 762 GLN Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 551 VAL Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 725 GLU Chi-restraints excluded: chain F residue 749 CYS Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 909 ILE Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 916 LEU Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1128 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 414 optimal weight: 0.9980 chunk 484 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 348 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 458 optimal weight: 4.9990 chunk 255 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 chunk 454 optimal weight: 3.9990 chunk 391 optimal weight: 5.9990 chunk 182 optimal weight: 40.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.111973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.067300 restraints weight = 398433.087| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 9.37 r_work: 0.2847 rms_B_bonded: 6.13 restraints_weight: 2.0000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2793 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2793 r_free = 0.2793 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2793 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 41362 Z= 0.147 Angle : 0.656 59.200 56404 Z= 0.336 Chirality : 0.042 0.360 6360 Planarity : 0.003 0.042 7199 Dihedral : 7.918 103.364 6568 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.93 % Allowed : 12.83 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 4928 helix: 1.94 (0.12), residues: 1791 sheet: -0.43 (0.17), residues: 818 loop : -0.28 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 192 TYR 0.019 0.001 TYR B1067 PHE 0.013 0.001 PHE D 898 TRP 0.013 0.001 TRP E 163 HIS 0.004 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00322 (41260) covalent geometry : angle 0.63789 (56143) SS BOND : bond 0.00253 ( 45) SS BOND : angle 1.04118 ( 90) hydrogen bonds : bond 0.03476 ( 1873) hydrogen bonds : angle 4.84222 ( 5303) link_BETA1-4 : bond 0.00912 ( 12) link_BETA1-4 : angle 3.19263 ( 36) link_NAG-ASN : bond 0.00389 ( 45) link_NAG-ASN : angle 2.67664 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 126 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6226 (mtm) REVERT: A 600 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7274 (tppt) REVERT: B 84 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8394 (mm) REVERT: B 104 TRP cc_start: 0.7773 (OUTLIER) cc_final: 0.6766 (t60) REVERT: B 365 TYR cc_start: 0.9365 (m-80) cc_final: 0.9104 (m-80) REVERT: B 955 ASN cc_start: 0.9334 (OUTLIER) cc_final: 0.8922 (t0) REVERT: C -1 VAL cc_start: 0.6985 (OUTLIER) cc_final: 0.6759 (m) REVERT: D 53 ASP cc_start: 0.9024 (t0) cc_final: 0.8780 (t0) REVERT: D 495 TYR cc_start: 0.4339 (OUTLIER) cc_final: 0.3183 (m-10) REVERT: D 568 ASP cc_start: 0.9083 (t0) cc_final: 0.8834 (t0) REVERT: D 762 GLN cc_start: 0.9334 (OUTLIER) cc_final: 0.8807 (pm20) REVERT: E 383 MET cc_start: 0.6074 (mtp) cc_final: 0.5267 (ttm) REVERT: F 725 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8744 (tt0) REVERT: F 909 ILE cc_start: 0.9521 (OUTLIER) cc_final: 0.9300 (tp) REVERT: F 1113 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8826 (pm20) outliers start: 80 outliers final: 65 residues processed: 197 average time/residue: 0.1777 time to fit residues: 63.6347 Evaluate side-chains 201 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 125 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue -1 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 762 GLN Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 551 VAL Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 725 GLU Chi-restraints excluded: chain F residue 749 CYS Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 909 ILE Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 916 LEU Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 379 optimal weight: 30.0000 chunk 475 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 432 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 365 optimal weight: 20.0000 chunk 444 optimal weight: 2.9990 chunk 254 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.111979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.067755 restraints weight = 349584.071| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 7.44 r_work: 0.2860 rms_B_bonded: 5.86 restraints_weight: 2.0000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 41362 Z= 0.147 Angle : 0.656 59.200 56404 Z= 0.336 Chirality : 0.042 0.360 6360 Planarity : 0.003 0.042 7199 Dihedral : 7.918 103.364 6568 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.84 % Allowed : 12.88 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 4928 helix: 1.94 (0.12), residues: 1791 sheet: -0.43 (0.17), residues: 818 loop : -0.28 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 192 TYR 0.019 0.001 TYR B1067 PHE 0.013 0.001 PHE D 898 TRP 0.013 0.001 TRP E 163 HIS 0.004 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00322 (41260) covalent geometry : angle 0.63789 (56143) SS BOND : bond 0.00253 ( 45) SS BOND : angle 1.04118 ( 90) hydrogen bonds : bond 0.03476 ( 1873) hydrogen bonds : angle 4.84222 ( 5303) link_BETA1-4 : bond 0.00912 ( 12) link_BETA1-4 : angle 3.19263 ( 36) link_NAG-ASN : bond 0.00389 ( 45) link_NAG-ASN : angle 2.67664 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9856 Ramachandran restraints generated. 4928 Oldfield, 0 Emsley, 4928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 125 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 579 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.5290 (mtm) REVERT: A 600 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7009 (tppt) REVERT: B 84 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8352 (mm) REVERT: B 104 TRP cc_start: 0.7759 (OUTLIER) cc_final: 0.6744 (t60) REVERT: B 365 TYR cc_start: 0.9383 (m-80) cc_final: 0.9127 (m-80) REVERT: B 955 ASN cc_start: 0.9316 (OUTLIER) cc_final: 0.8900 (t0) REVERT: C -1 VAL cc_start: 0.6818 (OUTLIER) cc_final: 0.6551 (m) REVERT: D 53 ASP cc_start: 0.8995 (t0) cc_final: 0.8756 (t0) REVERT: D 495 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.4165 (m-10) REVERT: D 568 ASP cc_start: 0.9078 (t0) cc_final: 0.8829 (t0) REVERT: D 762 GLN cc_start: 0.9330 (OUTLIER) cc_final: 0.8807 (pm20) REVERT: E 383 MET cc_start: 0.5825 (mtp) cc_final: 0.4807 (ttm) REVERT: F 725 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8704 (tt0) REVERT: F 909 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9298 (tp) REVERT: F 1113 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8829 (pm20) outliers start: 76 outliers final: 65 residues processed: 193 average time/residue: 0.2145 time to fit residues: 74.1304 Evaluate side-chains 201 residues out of total 4358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 125 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 519 HIS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 775 ASP Chi-restraints excluded: chain B residue 785 VAL Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 955 ASN Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1033 VAL Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue -1 VAL Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain D residue 42 VAL Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 88 ASP Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 495 TYR Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 699 LEU Chi-restraints excluded: chain D residue 762 GLN Chi-restraints excluded: chain D residue 780 GLU Chi-restraints excluded: chain D residue 915 VAL Chi-restraints excluded: chain D residue 934 ILE Chi-restraints excluded: chain D residue 968 SER Chi-restraints excluded: chain D residue 1033 VAL Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain E residue 581 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain F residue 367 VAL Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain F residue 523 THR Chi-restraints excluded: chain F residue 534 VAL Chi-restraints excluded: chain F residue 546 LEU Chi-restraints excluded: chain F residue 551 VAL Chi-restraints excluded: chain F residue 581 THR Chi-restraints excluded: chain F residue 645 THR Chi-restraints excluded: chain F residue 705 VAL Chi-restraints excluded: chain F residue 725 GLU Chi-restraints excluded: chain F residue 749 CYS Chi-restraints excluded: chain F residue 791 THR Chi-restraints excluded: chain F residue 909 ILE Chi-restraints excluded: chain F residue 915 VAL Chi-restraints excluded: chain F residue 916 LEU Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 998 THR Chi-restraints excluded: chain F residue 1033 VAL Chi-restraints excluded: chain F residue 1061 VAL Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1113 GLN Chi-restraints excluded: chain F residue 1128 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 495 random chunks: chunk 473 optimal weight: 1.9990 chunk 402 optimal weight: 9.9990 chunk 178 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 170 optimal weight: 0.0870 chunk 109 optimal weight: 9.9990 chunk 266 optimal weight: 0.0980 chunk 26 optimal weight: 40.0000 chunk 295 optimal weight: 6.9990 chunk 103 optimal weight: 50.0000 chunk 204 optimal weight: 40.0000 overall best weight: 3.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.111980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.068055 restraints weight = 374505.592| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 7.82 r_work: 0.2863 rms_B_bonded: 6.30 restraints_weight: 2.0000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 38 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 32 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.131 41362 Z= 0.147 Angle : 0.656 59.200 56404 Z= 0.336 Chirality : 0.042 0.360 6360 Planarity : 0.003 0.042 7199 Dihedral : 7.918 103.364 6568 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.84 % Allowed : 12.88 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 4928 helix: 1.94 (0.12), residues: 1791 sheet: -0.43 (0.17), residues: 818 loop : -0.28 (0.13), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 192 TYR 0.019 0.001 TYR B1067 PHE 0.013 0.001 PHE D 898 TRP 0.013 0.001 TRP E 163 HIS 0.004 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00322 (41260) covalent geometry : angle 0.63789 (56143) SS BOND : bond 0.00253 ( 45) SS BOND : angle 1.04118 ( 90) hydrogen bonds : bond 0.03476 ( 1873) hydrogen bonds : angle 4.84222 ( 5303) link_BETA1-4 : bond 0.00912 ( 12) link_BETA1-4 : angle 3.19263 ( 36) link_NAG-ASN : bond 0.00389 ( 45) link_NAG-ASN : angle 2.67664 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28281.39 seconds wall clock time: 478 minutes 24.08 seconds (28704.08 seconds total)