Starting phenix.real_space_refine on Fri Feb 6 17:10:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wg6_32478/02_2026/7wg6_32478.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wg6_32478/02_2026/7wg6_32478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wg6_32478/02_2026/7wg6_32478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wg6_32478/02_2026/7wg6_32478.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wg6_32478/02_2026/7wg6_32478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wg6_32478/02_2026/7wg6_32478.map" } resolution = 3.4 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= 0.005 sd= 0.094 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 117 5.16 5 C 17093 2.51 5 N 4370 2.21 5 O 5228 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s 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: 26808 Number of models: 1 Model: "" Number of chains: 27 Chain: "B" Number of atoms: 8611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8611 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "C" Number of atoms: 8586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8586 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 54, 'TRANS': 1037} Chain breaks: 6 Chain: "D" 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: "E" 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: "F" 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.70, per 1000 atoms: 0.25 Number of scatterers: 26808 At special positions: 0 Unit cell: (147.66, 138.03, 221.49, 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 117 16.00 O 5228 8.00 N 4370 7.00 C 17093 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.06 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=2.04 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 A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " 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 P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A1201 " - " ASN A 148 " " NAG A1202 " - " ASN A 17 " " NAG A1203 " - " ASN A 343 " " NAG A1204 " - " ASN A 61 " " NAG A1205 " - " ASN A 603 " " NAG A1206 " - " ASN A 657 " " NAG A1207 " - " ASN A 616 " " NAG A1208 " - " ASN A 709 " " NAG B1201 " - " ASN B 125 " " NAG B1202 " - " ASN B 17 " " NAG B1203 " - " ASN B 343 " " NAG B1204 " - " ASN B 61 " " NAG B1205 " - " ASN B 603 " " NAG B1206 " - " ASN B 657 " " NAG B1207 " - " ASN B 616 " " NAG B1208 " - " ASN B 709 " " NAG C1201 " - " ASN C 122 " " NAG C1202 " - " ASN C 17 " " NAG C1203 " - " ASN C 343 " " NAG C1204 " - " ASN C 61 " " NAG C1205 " - " ASN C 603 " " NAG C1206 " - " ASN C 657 " " NAG C1207 " - " ASN C 616 " " NAG C1208 " - " ASN C 709 " " NAG E 1 " - " ASN B 331 " " NAG F 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN A 236 " " NAG L 1 " - " ASN A 331 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A1098 " " NAG Q 1 " - " ASN A1134 " " NAG R 1 " - " ASN C 236 " " NAG S 1 " - " ASN C 331 " " NAG T 1 " - " ASN C 717 " " NAG U 1 " - " ASN C1074 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6186 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 46 sheets defined 24.9% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.825A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.134A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 5.113A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.770A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.637A pdb=" N THR B 638 " --> pdb=" O VAL B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 4.301A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.760A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 783 " --> pdb=" O GLN B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.675A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 856 removed outlier: 3.708A pdb=" N PHE B 855 " --> pdb=" O ALA B 852 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS B 856 " --> pdb=" O GLN B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 881 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.750A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.580A pdb=" N ASN B 925 " --> pdb=" O LYS B 921 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA B 930 " --> pdb=" O GLN B 926 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY B 932 " --> pdb=" O ASN B 928 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER B 937 " --> pdb=" O LYS B 933 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 3.934A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 984 removed outlier: 3.895A pdb=" N SER B 982 " --> pdb=" O ASN B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 1033 removed outlier: 4.137A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 4.278A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLU B1151 " --> pdb=" O SER B1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.549A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 411 removed outlier: 3.930A pdb=" N ALA A 411 " --> pdb=" O ARG A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.706A pdb=" N ASN A 422 " --> pdb=" O ILE A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 removed outlier: 3.929A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.516A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.740A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 783 " --> pdb=" O GLN A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 866 through 882 removed outlier: 3.535A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.695A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.786A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.685A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.676A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.105A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.842A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1033 removed outlier: 3.923A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1161 removed outlier: 5.113A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU A1151 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A1161 " --> pdb=" O LYS A1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.910A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.175A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 411 removed outlier: 4.251A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 411 " --> pdb=" O ARG C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 removed outlier: 3.645A pdb=" N ASN C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.622A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.961A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.624A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 783 " --> pdb=" O GLN C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 removed outlier: 3.707A pdb=" N ASP C 820 " --> pdb=" O SER C 816 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 882 removed outlier: 3.570A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.649A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.793A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.660A pdb=" N ASN C 925 " --> pdb=" O LYS C 921 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY C 932 " --> pdb=" O ASN C 928 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.960A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.036A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.453A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1161 removed outlier: 4.059A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER C1161 " --> pdb=" O LYS C1157 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.616A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 203 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 228 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 205 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 226 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.519A pdb=" N PHE B 55 " --> pdb=" O GLN B 271 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.146A pdb=" N ARG B 239 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE B 106 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN B 241 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TRP B 104 " --> pdb=" O GLN B 241 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU B 243 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.464A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.733A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.963A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'B' and resid 542 through 543 removed outlier: 3.815A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.597A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE B 565 " --> pdb=" O PHE A 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.370A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.354A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.637A pdb=" N ALA B 701 " --> pdb=" O ILE A 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'B' and resid 718 through 728 removed outlier: 3.562A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AB8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.678A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.792A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 203 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 229 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N SER A 205 " --> pdb=" O PRO A 227 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N HIS A 207 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N LEU A 225 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL A 36 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.731A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.799A pdb=" N PHE A 106 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 11.601A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.014A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.514A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.702A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.577A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.607A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 451 through 454 removed outlier: 4.661A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.993A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.234A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.746A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AD4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.996A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.718A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.725A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE C 203 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 229 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N SER C 205 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.887A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.559A pdb=" N ILE C 105 " --> pdb=" O GLN C 241 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.347A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 324 through 328 removed outlier: 3.968A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.784A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.949A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.655A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.619A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.542A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 735 through 736 removed outlier: 3.626A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.567A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2514 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: 5.85 Time building geometry restraints manager: 3.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4288 1.30 - 1.43: 7639 1.43 - 1.57: 15345 1.57 - 1.70: 0 1.70 - 1.83: 147 Bond restraints: 27419 Sorted by residual: bond pdb=" C PHE B 192 " pdb=" O PHE B 192 " ideal model delta sigma weight residual 1.234 1.169 0.065 1.18e-02 7.18e+03 3.04e+01 bond pdb=" CA SER B 205 " pdb=" CB SER B 205 " ideal model delta sigma weight residual 1.533 1.448 0.085 1.66e-02 3.63e+03 2.64e+01 bond pdb=" N ASP B 178 " pdb=" CA ASP B 178 " ideal model delta sigma weight residual 1.458 1.489 -0.031 6.30e-03 2.52e+04 2.39e+01 bond pdb=" C PHE B 194 " pdb=" O PHE B 194 " ideal model delta sigma weight residual 1.234 1.177 0.056 1.17e-02 7.31e+03 2.31e+01 bond pdb=" N ARG A 319 " pdb=" CA ARG A 319 " ideal model delta sigma weight residual 1.457 1.517 -0.059 1.29e-02 6.01e+03 2.12e+01 ... (remaining 27414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 36578 2.63 - 5.26: 614 5.26 - 7.90: 79 7.90 - 10.53: 10 10.53 - 13.16: 5 Bond angle restraints: 37286 Sorted by residual: angle pdb=" C GLU B 226 " pdb=" CA GLU B 226 " pdb=" CB GLU B 226 " ideal model delta sigma weight residual 108.68 97.06 11.62 1.39e+00 5.18e-01 6.99e+01 angle pdb=" N PRO A 322 " pdb=" CA PRO A 322 " pdb=" C PRO A 322 " ideal model delta sigma weight residual 110.80 122.28 -11.48 1.51e+00 4.39e-01 5.78e+01 angle pdb=" CA PHE B 201 " pdb=" C PHE B 201 " pdb=" O PHE B 201 " ideal model delta sigma weight residual 121.16 113.64 7.52 1.13e+00 7.83e-01 4.43e+01 angle pdb=" C ARG A 319 " pdb=" CA ARG A 319 " pdb=" CB ARG A 319 " ideal model delta sigma weight residual 110.42 97.26 13.16 1.99e+00 2.53e-01 4.37e+01 angle pdb=" CA PHE B 201 " pdb=" CB PHE B 201 " pdb=" CG PHE B 201 " ideal model delta sigma weight residual 113.80 120.25 -6.45 1.00e+00 1.00e+00 4.16e+01 ... (remaining 37281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.65: 16136 24.65 - 49.31: 932 49.31 - 73.96: 137 73.96 - 98.61: 49 98.61 - 123.27: 21 Dihedral angle restraints: 17275 sinusoidal: 7674 harmonic: 9601 Sorted by residual: dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 155.43 -62.43 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" C ILE B 210 " pdb=" N ILE B 210 " pdb=" CA ILE B 210 " pdb=" CB ILE B 210 " ideal model delta harmonic sigma weight residual -122.00 -139.83 17.83 0 2.50e+00 1.60e-01 5.09e+01 dihedral pdb=" C LYS B 202 " pdb=" N LYS B 202 " pdb=" CA LYS B 202 " pdb=" CB LYS B 202 " ideal model delta harmonic sigma weight residual -122.60 -104.85 -17.75 0 2.50e+00 1.60e-01 5.04e+01 ... (remaining 17272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 4283 0.124 - 0.247: 96 0.247 - 0.371: 25 0.371 - 0.494: 6 0.494 - 0.618: 4 Chirality restraints: 4414 Sorted by residual: chirality pdb=" CA ILE B 210 " pdb=" N ILE B 210 " pdb=" C ILE B 210 " pdb=" CB ILE B 210 " both_signs ideal model delta sigma weight residual False 2.43 1.82 0.62 2.00e-01 2.50e+01 9.53e+00 chirality pdb=" CA PRO B 227 " pdb=" N PRO B 227 " pdb=" C PRO B 227 " pdb=" CB PRO B 227 " both_signs ideal model delta sigma weight residual False 2.72 2.11 0.61 2.00e-01 2.50e+01 9.26e+00 chirality pdb=" CB VAL B 193 " pdb=" CA VAL B 193 " pdb=" CG1 VAL B 193 " pdb=" CG2 VAL B 193 " both_signs ideal model delta sigma weight residual False -2.63 -2.04 -0.59 2.00e-01 2.50e+01 8.58e+00 ... (remaining 4411 not shown) Planarity restraints: 4756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 318 " -0.022 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C PHE A 318 " 0.073 2.00e-02 2.50e+03 pdb=" O PHE A 318 " -0.027 2.00e-02 2.50e+03 pdb=" N ARG A 319 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 617 " 0.020 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C CYS C 617 " -0.067 2.00e-02 2.50e+03 pdb=" O CYS C 617 " 0.025 2.00e-02 2.50e+03 pdb=" N THR C 618 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 146 " -0.028 2.00e-02 2.50e+03 2.16e-02 7.00e+00 pdb=" CG HIS C 146 " 0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS C 146 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS C 146 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS C 146 " -0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS C 146 " -0.006 2.00e-02 2.50e+03 ... (remaining 4753 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 436 2.66 - 3.22: 24433 3.22 - 3.78: 37791 3.78 - 4.34: 50197 4.34 - 4.90: 84779 Nonbonded interactions: 197636 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.097 3.040 nonbonded pdb=" OG SER A 98 " pdb=" O GLU A 180 " model vdw 2.102 3.040 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.168 3.040 nonbonded pdb=" OD2 ASP C 398 " pdb=" OH TYR C 423 " model vdw 2.192 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OG1 THR B 114 " model vdw 2.207 3.040 ... (remaining 197631 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 14 through 140 or (resid 141 through 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 627 or resid 633 th \ rough 702 or resid 704 through 1208)) selection = (chain 'B' and (resid 14 through 627 or resid 633 through 702 or resid 704 throu \ gh 1208)) selection = (chain 'C' and (resid 14 through 140 or (resid 141 through 149 and (name N or na \ me CA or name C or name O or name CB )) or resid 150 through 1208)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'P' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.690 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 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 : 0.005 0.085 27530 Z= 0.288 Angle : 0.808 13.162 37571 Z= 0.461 Chirality : 0.059 0.618 4414 Planarity : 0.004 0.061 4713 Dihedral : 15.841 123.266 10972 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.33 % Favored : 93.33 % Rotamer: Outliers : 1.88 % Allowed : 1.11 % Favored : 97.01 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -1.13 (0.14), residues: 3254 helix: 0.91 (0.20), residues: 701 sheet: 0.08 (0.20), residues: 664 loop : -1.81 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.033 0.001 TYR B 204 PHE 0.033 0.001 PHE B 201 TRP 0.023 0.001 TRP C 64 HIS 0.010 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00478 (27419) covalent geometry : angle 0.78674 (37286) SS BOND : bond 0.00520 ( 39) SS BOND : angle 1.26841 ( 78) hydrogen bonds : bond 0.15310 ( 918) hydrogen bonds : angle 6.41411 ( 2514) Misc. bond : bond 0.00063 ( 3) link_BETA1-4 : bond 0.00469 ( 26) link_BETA1-4 : angle 1.81313 ( 78) link_NAG-ASN : bond 0.00458 ( 43) link_NAG-ASN : angle 2.83961 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 339 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.7795 (mt) cc_final: 0.7495 (mt) REVERT: B 150 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.6272 (tptp) REVERT: B 182 LYS cc_start: 0.0261 (OUTLIER) cc_final: -0.0022 (pptt) REVERT: B 216 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.5733 (mp0) REVERT: B 220 GLN cc_start: 0.7907 (tt0) cc_final: 0.7647 (tt0) REVERT: B 305 SER cc_start: 0.9194 (t) cc_final: 0.8843 (p) REVERT: B 467 ASP cc_start: 0.7548 (p0) cc_final: 0.7226 (p0) REVERT: B 523 THR cc_start: 0.8075 (m) cc_final: 0.7785 (p) REVERT: B 547 LYS cc_start: 0.8166 (mttt) cc_final: 0.7958 (mttp) REVERT: B 569 ILE cc_start: 0.8889 (tt) cc_final: 0.8685 (tt) REVERT: B 886 TRP cc_start: 0.8343 (p90) cc_final: 0.7983 (p90) REVERT: B 887 THR cc_start: 0.9145 (p) cc_final: 0.8815 (t) REVERT: A 134 GLN cc_start: 0.7784 (tp40) cc_final: 0.7476 (tm-30) REVERT: A 498 ARG cc_start: 0.7468 (ptp-110) cc_final: 0.7096 (mtm-85) REVERT: A 673 SER cc_start: 0.8418 (t) cc_final: 0.7702 (p) REVERT: A 814 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7364 (mmtp) REVERT: A 823 PHE cc_start: 0.7822 (m-80) cc_final: 0.7620 (m-80) REVERT: A 886 TRP cc_start: 0.7911 (p90) cc_final: 0.6957 (p90) REVERT: A 1005 GLN cc_start: 0.7363 (tp40) cc_final: 0.6924 (mt0) REVERT: C 30 ASN cc_start: 0.7940 (t0) cc_final: 0.7511 (p0) REVERT: C 52 GLN cc_start: 0.7614 (pm20) cc_final: 0.7295 (pt0) REVERT: C 314 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7290 (tt0) REVERT: C 540 ASN cc_start: 0.7297 (m-40) cc_final: 0.6956 (t0) REVERT: C 955 ASN cc_start: 0.7596 (t0) cc_final: 0.6915 (m-40) REVERT: C 1119 ASN cc_start: 0.7797 (m110) cc_final: 0.7519 (m-40) outliers start: 54 outliers final: 10 residues processed: 386 average time/residue: 0.1775 time to fit residues: 108.7487 Evaluate side-chains 224 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 LYS Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 622 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.0770 chunk 298 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN C 148 ASN C 188 ASN C 564 GLN C 625 HIS ** C1101 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 = 0.4114 r_free = 0.4114 target = 0.181586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157277 restraints weight = 34461.135| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.42 r_work: 0.3463 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 27530 Z= 0.174 Angle : 0.669 11.813 37571 Z= 0.332 Chirality : 0.048 0.431 4414 Planarity : 0.004 0.060 4713 Dihedral : 9.636 96.390 5043 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.48 % Favored : 93.42 % Rotamer: Outliers : 1.46 % Allowed : 9.79 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.14), residues: 3254 helix: 0.84 (0.20), residues: 727 sheet: 0.19 (0.20), residues: 689 loop : -1.82 (0.13), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 493 TYR 0.024 0.002 TYR B 160 PHE 0.025 0.002 PHE B 906 TRP 0.017 0.001 TRP C 64 HIS 0.008 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00416 (27419) covalent geometry : angle 0.64476 (37286) SS BOND : bond 0.00914 ( 39) SS BOND : angle 1.40404 ( 78) hydrogen bonds : bond 0.06291 ( 918) hydrogen bonds : angle 5.31722 ( 2514) Misc. bond : bond 0.00039 ( 3) link_BETA1-4 : bond 0.00611 ( 26) link_BETA1-4 : angle 2.00930 ( 78) link_NAG-ASN : bond 0.00458 ( 43) link_NAG-ASN : angle 2.55190 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 222 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.7983 (mt) cc_final: 0.7727 (mt) REVERT: B 981 PHE cc_start: 0.6741 (m-10) cc_final: 0.6371 (m-10) REVERT: A 200 TYR cc_start: 0.6458 (m-80) cc_final: 0.6146 (m-80) REVERT: A 569 ILE cc_start: 0.8912 (tp) cc_final: 0.8663 (tt) REVERT: A 673 SER cc_start: 0.8843 (t) cc_final: 0.8613 (p) REVERT: A 814 LYS cc_start: 0.7547 (mmtt) cc_final: 0.7209 (mmtm) REVERT: A 886 TRP cc_start: 0.8191 (p90) cc_final: 0.7904 (p90) REVERT: A 1005 GLN cc_start: 0.8267 (tp40) cc_final: 0.8034 (mt0) REVERT: C 52 GLN cc_start: 0.7798 (pm20) cc_final: 0.7556 (tt0) REVERT: C 314 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: C 955 ASN cc_start: 0.8153 (t0) cc_final: 0.7830 (m-40) outliers start: 42 outliers final: 27 residues processed: 252 average time/residue: 0.1525 time to fit residues: 64.6059 Evaluate side-chains 207 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 256 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 321 optimal weight: 0.9990 chunk 311 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 82 optimal weight: 0.0060 chunk 116 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 278 optimal weight: 4.9990 chunk 194 optimal weight: 0.5980 chunk 155 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 121 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN C 625 HIS C 955 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.182357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.158852 restraints weight = 34364.319| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.30 r_work: 0.3503 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 27530 Z= 0.136 Angle : 0.618 11.785 37571 Z= 0.305 Chirality : 0.046 0.412 4414 Planarity : 0.004 0.065 4713 Dihedral : 7.622 92.698 5026 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.65 % Favored : 94.28 % Rotamer: Outliers : 1.60 % Allowed : 12.08 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.88 (0.14), residues: 3254 helix: 1.07 (0.20), residues: 713 sheet: 0.30 (0.20), residues: 673 loop : -1.68 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 454 TYR 0.019 0.001 TYR A1067 PHE 0.016 0.001 PHE B 906 TRP 0.013 0.001 TRP C 64 HIS 0.010 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00318 (27419) covalent geometry : angle 0.59420 (37286) SS BOND : bond 0.00307 ( 39) SS BOND : angle 1.25432 ( 78) hydrogen bonds : bond 0.05691 ( 918) hydrogen bonds : angle 5.04839 ( 2514) Misc. bond : bond 0.00026 ( 3) link_BETA1-4 : bond 0.00557 ( 26) link_BETA1-4 : angle 1.88017 ( 78) link_NAG-ASN : bond 0.00435 ( 43) link_NAG-ASN : angle 2.43639 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 467 ASP cc_start: 0.7818 (p0) cc_final: 0.7579 (p0) REVERT: B 886 TRP cc_start: 0.8819 (p90) cc_final: 0.8341 (p90) REVERT: B 965 GLN cc_start: 0.8623 (tt0) cc_final: 0.8372 (tp40) REVERT: B 981 PHE cc_start: 0.6675 (m-10) cc_final: 0.6400 (m-10) REVERT: A 569 ILE cc_start: 0.8877 (tp) cc_final: 0.8636 (tt) REVERT: A 673 SER cc_start: 0.8776 (t) cc_final: 0.8553 (p) REVERT: A 814 LYS cc_start: 0.7554 (mmtt) cc_final: 0.7218 (mmtm) REVERT: A 886 TRP cc_start: 0.8249 (p90) cc_final: 0.7989 (p90) REVERT: A 1005 GLN cc_start: 0.8415 (tp40) cc_final: 0.8181 (mt0) REVERT: C 314 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7803 (tt0) REVERT: C 752 LEU cc_start: 0.8723 (tt) cc_final: 0.8327 (mt) REVERT: C 955 ASN cc_start: 0.8320 (t0) cc_final: 0.8040 (m-40) outliers start: 46 outliers final: 30 residues processed: 235 average time/residue: 0.1590 time to fit residues: 63.6260 Evaluate side-chains 210 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 314 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 209 optimal weight: 0.4980 chunk 169 optimal weight: 4.9990 chunk 259 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 34 optimal weight: 0.1980 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 275 optimal weight: 0.0670 chunk 30 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 109 optimal weight: 30.0000 overall best weight: 1.3522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS B1119 ASN A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 625 HIS ** C1101 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 = 0.4092 r_free = 0.4092 target = 0.179545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156507 restraints weight = 34351.630| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.31 r_work: 0.3461 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 27530 Z= 0.181 Angle : 0.640 11.835 37571 Z= 0.318 Chirality : 0.047 0.416 4414 Planarity : 0.004 0.056 4713 Dihedral : 6.906 91.791 5017 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.64 % Favored : 93.30 % Rotamer: Outliers : 2.36 % Allowed : 14.51 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.96 (0.14), residues: 3254 helix: 0.92 (0.20), residues: 720 sheet: 0.21 (0.20), residues: 685 loop : -1.69 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 905 TYR 0.019 0.002 TYR A1067 PHE 0.020 0.002 PHE B 133 TRP 0.018 0.001 TRP C 64 HIS 0.017 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00449 (27419) covalent geometry : angle 0.61608 (37286) SS BOND : bond 0.00324 ( 39) SS BOND : angle 1.32641 ( 78) hydrogen bonds : bond 0.06440 ( 918) hydrogen bonds : angle 5.07484 ( 2514) Misc. bond : bond 0.00029 ( 3) link_BETA1-4 : bond 0.00480 ( 26) link_BETA1-4 : angle 1.83598 ( 78) link_NAG-ASN : bond 0.00415 ( 43) link_NAG-ASN : angle 2.55579 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 171 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 467 ASP cc_start: 0.7834 (p0) cc_final: 0.7617 (p0) REVERT: B 886 TRP cc_start: 0.8840 (p90) cc_final: 0.8540 (p90) REVERT: B 981 PHE cc_start: 0.6720 (m-10) cc_final: 0.6438 (m-10) REVERT: A 351 TYR cc_start: 0.8568 (p90) cc_final: 0.8249 (p90) REVERT: A 569 ILE cc_start: 0.8914 (tp) cc_final: 0.8659 (tt) REVERT: A 673 SER cc_start: 0.8820 (t) cc_final: 0.8589 (p) REVERT: A 779 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8455 (tm-30) REVERT: A 814 LYS cc_start: 0.7576 (mmtt) cc_final: 0.7240 (mmtm) REVERT: A 886 TRP cc_start: 0.8385 (p90) cc_final: 0.7994 (p90) REVERT: A 1005 GLN cc_start: 0.8469 (tp40) cc_final: 0.8219 (mt0) REVERT: C 955 ASN cc_start: 0.8366 (t0) cc_final: 0.8036 (m110) outliers start: 68 outliers final: 51 residues processed: 227 average time/residue: 0.1597 time to fit residues: 61.5811 Evaluate side-chains 216 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 238 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 98 optimal weight: 0.9990 chunk 318 optimal weight: 2.9990 chunk 290 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 132 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 309 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 183 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 ASN A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.179961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156426 restraints weight = 34236.137| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 2.33 r_work: 0.3473 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27530 Z= 0.155 Angle : 0.612 11.903 37571 Z= 0.303 Chirality : 0.046 0.407 4414 Planarity : 0.004 0.054 4713 Dihedral : 6.528 91.709 5013 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 2.33 % Allowed : 15.59 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.92 (0.14), residues: 3254 helix: 1.01 (0.20), residues: 718 sheet: 0.23 (0.20), residues: 685 loop : -1.68 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 905 TYR 0.019 0.001 TYR A1067 PHE 0.015 0.001 PHE A1121 TRP 0.013 0.001 TRP C 64 HIS 0.017 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00377 (27419) covalent geometry : angle 0.58731 (37286) SS BOND : bond 0.00310 ( 39) SS BOND : angle 1.33307 ( 78) hydrogen bonds : bond 0.06058 ( 918) hydrogen bonds : angle 5.00343 ( 2514) Misc. bond : bond 0.00069 ( 3) link_BETA1-4 : bond 0.00496 ( 26) link_BETA1-4 : angle 1.79515 ( 78) link_NAG-ASN : bond 0.00397 ( 43) link_NAG-ASN : angle 2.48761 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 175 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8708 (mm) cc_final: 0.8211 (mt) REVERT: B 335 LEU cc_start: 0.8775 (mm) cc_final: 0.8177 (tt) REVERT: B 981 PHE cc_start: 0.6615 (m-10) cc_final: 0.6380 (m-10) REVERT: A 351 TYR cc_start: 0.8544 (p90) cc_final: 0.8229 (p90) REVERT: A 428 ASP cc_start: 0.8236 (p0) cc_final: 0.8031 (p0) REVERT: A 569 ILE cc_start: 0.8874 (tp) cc_final: 0.8631 (tt) REVERT: A 673 SER cc_start: 0.8703 (t) cc_final: 0.8481 (p) REVERT: A 779 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8292 (tm-30) REVERT: A 814 LYS cc_start: 0.7491 (mmtt) cc_final: 0.7166 (mmtm) REVERT: A 886 TRP cc_start: 0.8372 (p90) cc_final: 0.7963 (p90) REVERT: A 1005 GLN cc_start: 0.8385 (tp40) cc_final: 0.8167 (mt0) REVERT: C 200 TYR cc_start: 0.8126 (m-80) cc_final: 0.7886 (m-80) REVERT: C 207 HIS cc_start: 0.7243 (t-90) cc_final: 0.7003 (t70) REVERT: C 955 ASN cc_start: 0.8216 (t0) cc_final: 0.7935 (m110) outliers start: 67 outliers final: 47 residues processed: 236 average time/residue: 0.1530 time to fit residues: 61.7736 Evaluate side-chains 216 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 77 optimal weight: 0.7980 chunk 97 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 50 optimal weight: 0.0870 chunk 255 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 204 optimal weight: 2.9990 chunk 205 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 422 ASN A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 137 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.182148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158154 restraints weight = 34182.903| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.41 r_work: 0.3478 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27530 Z= 0.111 Angle : 0.569 11.216 37571 Z= 0.281 Chirality : 0.044 0.411 4414 Planarity : 0.004 0.052 4713 Dihedral : 6.150 90.843 5013 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.72 % Favored : 94.22 % Rotamer: Outliers : 2.08 % Allowed : 16.22 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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 (0.15), residues: 3254 helix: 1.30 (0.20), residues: 712 sheet: 0.32 (0.20), residues: 684 loop : -1.60 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 498 TYR 0.018 0.001 TYR B 453 PHE 0.024 0.001 PHE B 133 TRP 0.011 0.001 TRP C 64 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00245 (27419) covalent geometry : angle 0.54534 (37286) SS BOND : bond 0.00251 ( 39) SS BOND : angle 1.17074 ( 78) hydrogen bonds : bond 0.05122 ( 918) hydrogen bonds : angle 4.79832 ( 2514) Misc. bond : bond 0.00022 ( 3) link_BETA1-4 : bond 0.00519 ( 26) link_BETA1-4 : angle 1.76113 ( 78) link_NAG-ASN : bond 0.00453 ( 43) link_NAG-ASN : angle 2.38069 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 187 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8688 (mm) cc_final: 0.8204 (mt) REVERT: B 335 LEU cc_start: 0.8751 (mm) cc_final: 0.8121 (tt) REVERT: B 465 GLU cc_start: 0.7261 (tt0) cc_final: 0.6975 (tt0) REVERT: B 965 GLN cc_start: 0.8651 (tt0) cc_final: 0.8419 (tp40) REVERT: B 981 PHE cc_start: 0.6620 (m-10) cc_final: 0.6402 (m-10) REVERT: A 569 ILE cc_start: 0.8852 (tp) cc_final: 0.8619 (tt) REVERT: A 673 SER cc_start: 0.8799 (t) cc_final: 0.8567 (p) REVERT: A 814 LYS cc_start: 0.7616 (mmtt) cc_final: 0.7261 (mmtm) REVERT: A 886 TRP cc_start: 0.8410 (p90) cc_final: 0.8003 (p90) REVERT: A 1005 GLN cc_start: 0.8491 (tp40) cc_final: 0.8248 (mt0) REVERT: C 200 TYR cc_start: 0.8174 (m-80) cc_final: 0.7945 (m-80) REVERT: C 207 HIS cc_start: 0.7236 (t-90) cc_final: 0.7016 (t70) REVERT: C 321 GLN cc_start: 0.5963 (OUTLIER) cc_final: 0.5429 (pt0) REVERT: C 955 ASN cc_start: 0.8279 (t0) cc_final: 0.7949 (m110) outliers start: 60 outliers final: 40 residues processed: 242 average time/residue: 0.1579 time to fit residues: 65.5027 Evaluate side-chains 216 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 274 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 254 optimal weight: 40.0000 chunk 73 optimal weight: 1.9990 chunk 269 optimal weight: 0.7980 chunk 238 optimal weight: 2.9990 chunk 259 optimal weight: 30.0000 chunk 124 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 196 ASN C 321 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.178436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.155151 restraints weight = 34071.258| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.31 r_work: 0.3448 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 27530 Z= 0.200 Angle : 0.651 11.287 37571 Z= 0.323 Chirality : 0.047 0.399 4414 Planarity : 0.004 0.054 4713 Dihedral : 6.228 89.921 5013 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.55 % Rotamer: Outliers : 2.85 % Allowed : 16.22 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.91 (0.14), residues: 3254 helix: 1.11 (0.20), residues: 706 sheet: 0.23 (0.20), residues: 685 loop : -1.71 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 905 TYR 0.020 0.002 TYR B 453 PHE 0.028 0.002 PHE C 65 TRP 0.013 0.001 TRP C 64 HIS 0.028 0.002 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00502 (27419) covalent geometry : angle 0.62760 (37286) SS BOND : bond 0.00380 ( 39) SS BOND : angle 1.48185 ( 78) hydrogen bonds : bond 0.06600 ( 918) hydrogen bonds : angle 5.00066 ( 2514) Misc. bond : bond 0.00028 ( 3) link_BETA1-4 : bond 0.00480 ( 26) link_BETA1-4 : angle 1.76998 ( 78) link_NAG-ASN : bond 0.00381 ( 43) link_NAG-ASN : angle 2.51299 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 175 time to evaluate : 1.045 Fit side-chains REVERT: B 128 ILE cc_start: 0.8740 (mm) cc_final: 0.8257 (mt) REVERT: B 981 PHE cc_start: 0.6695 (m-10) cc_final: 0.6415 (m-10) REVERT: A 317 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7980 (m-40) REVERT: A 351 TYR cc_start: 0.8586 (p90) cc_final: 0.8329 (p90) REVERT: A 428 ASP cc_start: 0.8341 (p0) cc_final: 0.8133 (p0) REVERT: A 569 ILE cc_start: 0.8851 (tp) cc_final: 0.8606 (tt) REVERT: A 673 SER cc_start: 0.8771 (t) cc_final: 0.8561 (p) REVERT: A 779 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8532 (tm-30) REVERT: A 814 LYS cc_start: 0.7596 (mmtt) cc_final: 0.7266 (mmtm) REVERT: A 1005 GLN cc_start: 0.8535 (tp40) cc_final: 0.8266 (mt0) REVERT: C 200 TYR cc_start: 0.8248 (m-80) cc_final: 0.8013 (m-80) REVERT: C 207 HIS cc_start: 0.7189 (t-90) cc_final: 0.6977 (t70) REVERT: C 218 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7729 (mt) REVERT: C 569 ILE cc_start: 0.7900 (OUTLIER) cc_final: 0.7368 (mp) REVERT: C 955 ASN cc_start: 0.8376 (t0) cc_final: 0.8087 (m110) outliers start: 82 outliers final: 61 residues processed: 251 average time/residue: 0.1527 time to fit residues: 65.9903 Evaluate side-chains 230 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 166 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 121 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 169 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 279 optimal weight: 0.6980 chunk 161 optimal weight: 0.5980 chunk 136 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 30.0000 chunk 244 optimal weight: 0.5980 chunk 48 optimal weight: 0.0470 chunk 23 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C1101 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 = 0.4108 r_free = 0.4108 target = 0.181163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.154545 restraints weight = 34388.050| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.67 r_work: 0.3395 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27530 Z= 0.117 Angle : 0.582 11.048 37571 Z= 0.288 Chirality : 0.045 0.390 4414 Planarity : 0.004 0.053 4713 Dihedral : 5.952 90.353 5010 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.38 % Favored : 94.56 % Rotamer: Outliers : 1.94 % Allowed : 17.33 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.75 (0.14), residues: 3254 helix: 1.34 (0.20), residues: 706 sheet: 0.29 (0.20), residues: 698 loop : -1.64 (0.13), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 498 TYR 0.020 0.001 TYR B 453 PHE 0.026 0.001 PHE B 133 TRP 0.010 0.001 TRP C 64 HIS 0.014 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00262 (27419) covalent geometry : angle 0.55989 (37286) SS BOND : bond 0.00270 ( 39) SS BOND : angle 1.05895 ( 78) hydrogen bonds : bond 0.05344 ( 918) hydrogen bonds : angle 4.83434 ( 2514) Misc. bond : bond 0.00030 ( 3) link_BETA1-4 : bond 0.00502 ( 26) link_BETA1-4 : angle 1.76087 ( 78) link_NAG-ASN : bond 0.00422 ( 43) link_NAG-ASN : angle 2.36797 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 182 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8689 (mm) cc_final: 0.8254 (mt) REVERT: B 335 LEU cc_start: 0.8789 (mm) cc_final: 0.8106 (tt) REVERT: B 981 PHE cc_start: 0.6785 (m-10) cc_final: 0.6526 (m-10) REVERT: A 317 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7932 (m-40) REVERT: A 351 TYR cc_start: 0.8602 (p90) cc_final: 0.8288 (p90) REVERT: A 569 ILE cc_start: 0.8883 (tp) cc_final: 0.8632 (tt) REVERT: A 673 SER cc_start: 0.8704 (t) cc_final: 0.8475 (p) REVERT: A 814 LYS cc_start: 0.7628 (mmtt) cc_final: 0.7276 (mmtm) REVERT: A 1005 GLN cc_start: 0.8509 (tp40) cc_final: 0.8240 (mt0) REVERT: C 200 TYR cc_start: 0.8233 (m-80) cc_final: 0.7995 (m-80) REVERT: C 207 HIS cc_start: 0.7191 (t-90) cc_final: 0.6989 (t70) REVERT: C 218 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7692 (mt) REVERT: C 321 GLN cc_start: 0.6094 (OUTLIER) cc_final: 0.5211 (pt0) REVERT: C 955 ASN cc_start: 0.8258 (t0) cc_final: 0.7951 (m110) outliers start: 56 outliers final: 48 residues processed: 236 average time/residue: 0.1533 time to fit residues: 62.3663 Evaluate side-chains 225 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 174 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 61 optimal weight: 4.9990 chunk 192 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 272 optimal weight: 0.9980 chunk 235 optimal weight: 0.7980 chunk 226 optimal weight: 4.9990 chunk 302 optimal weight: 0.0770 chunk 86 optimal weight: 2.9990 chunk 234 optimal weight: 0.9990 chunk 256 optimal weight: 30.0000 chunk 139 optimal weight: 0.1980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C1101 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 = 0.4116 r_free = 0.4116 target = 0.181927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.157348 restraints weight = 34182.396| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.41 r_work: 0.3468 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27530 Z= 0.115 Angle : 0.572 10.968 37571 Z= 0.282 Chirality : 0.044 0.386 4414 Planarity : 0.004 0.053 4713 Dihedral : 5.689 88.198 5010 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.81 % Favored : 94.13 % Rotamer: Outliers : 2.12 % Allowed : 17.53 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.64 (0.15), residues: 3254 helix: 1.44 (0.20), residues: 713 sheet: 0.39 (0.20), residues: 695 loop : -1.59 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 498 TYR 0.019 0.001 TYR B 453 PHE 0.015 0.001 PHE A1121 TRP 0.011 0.001 TRP C 64 HIS 0.011 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00260 (27419) covalent geometry : angle 0.55030 (37286) SS BOND : bond 0.00252 ( 39) SS BOND : angle 1.00475 ( 78) hydrogen bonds : bond 0.05055 ( 918) hydrogen bonds : angle 4.69956 ( 2514) Misc. bond : bond 0.00020 ( 3) link_BETA1-4 : bond 0.00501 ( 26) link_BETA1-4 : angle 1.73606 ( 78) link_NAG-ASN : bond 0.00402 ( 43) link_NAG-ASN : angle 2.33228 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 181 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8666 (mm) cc_final: 0.8236 (mt) REVERT: B 335 LEU cc_start: 0.8715 (mm) cc_final: 0.8087 (tt) REVERT: B 465 GLU cc_start: 0.7206 (tt0) cc_final: 0.6926 (tt0) REVERT: A 317 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7870 (m-40) REVERT: A 428 ASP cc_start: 0.8389 (p0) cc_final: 0.8179 (p0) REVERT: A 673 SER cc_start: 0.8673 (t) cc_final: 0.8450 (p) REVERT: A 814 LYS cc_start: 0.7499 (mmtt) cc_final: 0.7175 (mmtm) REVERT: A 1005 GLN cc_start: 0.8373 (tp40) cc_final: 0.8163 (mt0) REVERT: C 207 HIS cc_start: 0.6966 (t-90) cc_final: 0.6740 (t70) REVERT: C 218 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7745 (mt) REVERT: C 955 ASN cc_start: 0.8150 (t0) cc_final: 0.7888 (m-40) outliers start: 61 outliers final: 53 residues processed: 237 average time/residue: 0.1560 time to fit residues: 63.6711 Evaluate side-chains 225 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 98 optimal weight: 2.9990 chunk 298 optimal weight: 0.6980 chunk 271 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 296 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.179229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.155783 restraints weight = 34097.633| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.32 r_work: 0.3467 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27530 Z= 0.170 Angle : 0.622 11.045 37571 Z= 0.308 Chirality : 0.046 0.387 4414 Planarity : 0.004 0.054 4713 Dihedral : 5.819 87.070 5010 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.39 % Favored : 93.55 % Rotamer: Outliers : 2.26 % Allowed : 17.47 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.82 (0.14), residues: 3254 helix: 1.22 (0.20), residues: 721 sheet: 0.31 (0.20), residues: 699 loop : -1.71 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 498 TYR 0.019 0.001 TYR B 453 PHE 0.021 0.002 PHE B 140 TRP 0.013 0.001 TRP C 633 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00420 (27419) covalent geometry : angle 0.59957 (37286) SS BOND : bond 0.00314 ( 39) SS BOND : angle 1.33746 ( 78) hydrogen bonds : bond 0.06144 ( 918) hydrogen bonds : angle 4.86316 ( 2514) Misc. bond : bond 0.00026 ( 3) link_BETA1-4 : bond 0.00485 ( 26) link_BETA1-4 : angle 1.75075 ( 78) link_NAG-ASN : bond 0.00371 ( 43) link_NAG-ASN : angle 2.42413 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 169 time to evaluate : 1.129 Fit side-chains REVERT: B 128 ILE cc_start: 0.8692 (mm) cc_final: 0.8379 (mt) REVERT: B 335 LEU cc_start: 0.8743 (mm) cc_final: 0.8128 (tt) REVERT: A 217 ASP cc_start: 0.6499 (t70) cc_final: 0.6245 (t70) REVERT: A 317 ASN cc_start: 0.8256 (OUTLIER) cc_final: 0.7947 (m-40) REVERT: A 351 TYR cc_start: 0.8598 (p90) cc_final: 0.8332 (p90) REVERT: A 673 SER cc_start: 0.8788 (t) cc_final: 0.8568 (p) REVERT: A 814 LYS cc_start: 0.7581 (mmtt) cc_final: 0.7266 (mmtm) REVERT: A 1005 GLN cc_start: 0.8507 (tp40) cc_final: 0.8255 (mt0) REVERT: C 218 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8002 (mt) REVERT: C 569 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7432 (mp) REVERT: C 955 ASN cc_start: 0.8352 (t0) cc_final: 0.8052 (m110) outliers start: 65 outliers final: 55 residues processed: 227 average time/residue: 0.1534 time to fit residues: 60.4540 Evaluate side-chains 223 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 165 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 909 ILE Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 98 SER Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 911 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 142 optimal weight: 1.9990 chunk 151 optimal weight: 8.9990 chunk 321 optimal weight: 0.0980 chunk 229 optimal weight: 0.7980 chunk 22 optimal weight: 30.0000 chunk 197 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 chunk 59 optimal weight: 0.5980 chunk 112 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN A 66 HIS ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN C 207 HIS ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1159 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.182124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.157214 restraints weight = 33909.137| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.44 r_work: 0.3465 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27530 Z= 0.109 Angle : 0.573 10.816 37571 Z= 0.282 Chirality : 0.044 0.375 4414 Planarity : 0.004 0.052 4713 Dihedral : 5.601 85.925 5010 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.22 % Favored : 94.71 % Rotamer: Outliers : 2.05 % Allowed : 17.67 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.64 (0.15), residues: 3254 helix: 1.43 (0.20), residues: 723 sheet: 0.38 (0.20), residues: 687 loop : -1.59 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 498 TYR 0.022 0.001 TYR B 508 PHE 0.020 0.001 PHE B 133 TRP 0.010 0.001 TRP C 633 HIS 0.006 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00241 (27419) covalent geometry : angle 0.55191 (37286) SS BOND : bond 0.00238 ( 39) SS BOND : angle 0.98182 ( 78) hydrogen bonds : bond 0.04970 ( 918) hydrogen bonds : angle 4.67837 ( 2514) Misc. bond : bond 0.00021 ( 3) link_BETA1-4 : bond 0.00500 ( 26) link_BETA1-4 : angle 1.75055 ( 78) link_NAG-ASN : bond 0.00404 ( 43) link_NAG-ASN : angle 2.30034 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5278.69 seconds wall clock time: 91 minutes 53.07 seconds (5513.07 seconds total)