Starting phenix.real_space_refine on Mon Jun 23 08:23:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wg6_32478/06_2025/7wg6_32478.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wg6_32478/06_2025/7wg6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wg6_32478/06_2025/7wg6_32478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wg6_32478/06_2025/7wg6_32478.map" model { file = "/net/cci-nas-00/data/ceres_data/7wg6_32478/06_2025/7wg6_32478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wg6_32478/06_2025/7wg6_32478.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'HIS:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} 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: 16.16, per 1000 atoms: 0.60 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: 7.05 Conformation dependent library (CDL) restraints added in 3.2 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: 3.82 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: 11.12 Time building geometry restraints manager: 8.13 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 1162 or resid 1201 through 1208)) selection = (chain 'B' and (resid 14 through 627 or resid 633 through 702 or resid 704 throu \ gh 1162 or resid 1201 through 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 1162 or resid 1201 \ 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: 7.310 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: 0.050 Extract box with map and model: 1.050 Check model and map are aligned: 0.210 Set scattering table: 0.220 Process input model: 61.270 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.750 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.023 0.001 TRP C 64 HIS 0.010 0.001 HIS C 146 PHE 0.033 0.001 PHE B 201 TYR 0.033 0.001 TYR B 204 ARG 0.002 0.000 ARG A 466 Details of bonding type rmsd link_NAG-ASN : bond 0.00458 ( 43) link_NAG-ASN : angle 2.83961 ( 129) link_BETA1-4 : bond 0.00469 ( 26) link_BETA1-4 : angle 1.81313 ( 78) hydrogen bonds : bond 0.15310 ( 918) hydrogen bonds : angle 6.41411 ( 2514) SS BOND : bond 0.00520 ( 39) SS BOND : angle 1.26841 ( 78) covalent geometry : bond 0.00478 (27419) covalent geometry : angle 0.78674 (37286) Misc. bond : bond 0.00063 ( 3) *********************** 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 : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.7795 (mt) cc_final: 0.7495 (mt) REVERT: B 150 LYS cc_start: 0.7584 (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: 0.7684 (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: 0.7224 (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: 0.8344 (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: 0.7941 (t0) cc_final: 0.7519 (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: 0.6914 (m-40) REVERT: C 1119 ASN cc_start: 0.7797 (m110) cc_final: 0.7518 (m-40) outliers start: 54 outliers final: 10 residues processed: 386 average time/residue: 0.3771 time to fit residues: 230.2778 Evaluate side-chains 226 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 2.675 ------------------------------------------------------------------------------- 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 276 optimal weight: 0.9980 chunk 247 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 167 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 256 optimal weight: 0.0170 chunk 99 optimal weight: 0.0070 chunk 155 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 296 optimal weight: 1.9990 overall best weight: 0.7438 ------------------------------------------------------------------------------- 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** A1010 GLN C 148 ASN C 188 ASN C 625 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.183386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.159187 restraints weight = 34159.061| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.39 r_work: 0.3497 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27530 Z= 0.138 Angle : 0.635 11.602 37571 Z= 0.316 Chirality : 0.046 0.419 4414 Planarity : 0.004 0.057 4713 Dihedral : 9.927 98.375 5043 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.02 % Favored : 93.88 % Rotamer: Outliers : 1.35 % Allowed : 8.58 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3254 helix: 1.03 (0.20), residues: 721 sheet: 0.25 (0.20), residues: 671 loop : -1.74 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 64 HIS 0.008 0.001 HIS B 66 PHE 0.022 0.001 PHE B 133 TYR 0.025 0.001 TYR B 160 ARG 0.006 0.000 ARG B 493 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 43) link_NAG-ASN : angle 2.48321 ( 129) link_BETA1-4 : bond 0.00646 ( 26) link_BETA1-4 : angle 1.95349 ( 78) hydrogen bonds : bond 0.05795 ( 918) hydrogen bonds : angle 5.28723 ( 2514) SS BOND : bond 0.00368 ( 39) SS BOND : angle 1.39878 ( 78) covalent geometry : bond 0.00316 (27419) covalent geometry : angle 0.61118 (37286) Misc. bond : bond 0.00020 ( 3) *********************** 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: 39 poor density : 225 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 LEU cc_start: 0.8024 (mt) cc_final: 0.7764 (mt) REVERT: B 886 TRP cc_start: 0.8631 (p90) cc_final: 0.8284 (p90) REVERT: B 981 PHE cc_start: 0.6738 (m-10) cc_final: 0.6378 (m-10) REVERT: B 1050 MET cc_start: 0.8435 (ptm) cc_final: 0.8199 (ptm) REVERT: A 177 MET cc_start: 0.1407 (mmp) cc_final: 0.0690 (ptt) REVERT: A 569 ILE cc_start: 0.8861 (tp) cc_final: 0.8602 (tt) REVERT: A 673 SER cc_start: 0.8789 (t) cc_final: 0.8547 (p) REVERT: A 886 TRP cc_start: 0.8180 (p90) cc_final: 0.7917 (p90) REVERT: C 33 THR cc_start: 0.7125 (p) cc_final: 0.6852 (p) REVERT: C 52 GLN cc_start: 0.7779 (pm20) cc_final: 0.7527 (tt0) REVERT: C 314 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: C 955 ASN cc_start: 0.8112 (t0) cc_final: 0.7786 (m-40) outliers start: 39 outliers final: 22 residues processed: 253 average time/residue: 0.3982 time to fit residues: 171.5930 Evaluate side-chains 213 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 2.693 ------------------------------------------------------------------------------- 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 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 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 238 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 309 GLU 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 257 optimal weight: 20.0000 chunk 282 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 288 optimal weight: 3.9990 chunk 313 optimal weight: 1.9990 chunk 278 optimal weight: 0.7980 chunk 284 optimal weight: 0.9980 chunk 255 optimal weight: 30.0000 chunk 314 optimal weight: 0.7980 chunk 208 optimal weight: 1.9990 chunk 154 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 99 ASN 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 751 ASN C 66 HIS C 625 HIS C 955 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.181143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158293 restraints weight = 34219.456| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.27 r_work: 0.3494 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 27530 Z= 0.161 Angle : 0.646 11.897 37571 Z= 0.320 Chirality : 0.047 0.416 4414 Planarity : 0.004 0.058 4713 Dihedral : 7.569 91.207 5024 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.27 % Favored : 93.64 % Rotamer: Outliers : 1.84 % Allowed : 11.91 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3254 helix: 1.03 (0.20), residues: 713 sheet: 0.26 (0.20), residues: 675 loop : -1.70 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 64 HIS 0.011 0.001 HIS B 207 PHE 0.028 0.002 PHE B 906 TYR 0.020 0.002 TYR A1067 ARG 0.006 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00428 ( 43) link_NAG-ASN : angle 2.53876 ( 129) link_BETA1-4 : bond 0.00550 ( 26) link_BETA1-4 : angle 1.86740 ( 78) hydrogen bonds : bond 0.06217 ( 918) hydrogen bonds : angle 5.12114 ( 2514) SS BOND : bond 0.00356 ( 39) SS BOND : angle 1.41008 ( 78) covalent geometry : bond 0.00388 (27419) covalent geometry : angle 0.62232 (37286) Misc. bond : bond 0.00164 ( 3) *********************** 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 246 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 193 time to evaluate : 3.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 886 TRP cc_start: 0.8835 (p90) cc_final: 0.8411 (p90) REVERT: B 981 PHE cc_start: 0.6657 (m-10) cc_final: 0.6393 (m-10) REVERT: A 569 ILE cc_start: 0.8904 (tp) cc_final: 0.8665 (tt) REVERT: A 673 SER cc_start: 0.8813 (t) cc_final: 0.8604 (p) REVERT: A 779 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8441 (tm-30) REVERT: A 814 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7214 (mmtm) REVERT: A 886 TRP cc_start: 0.8239 (p90) cc_final: 0.7985 (p90) REVERT: C 314 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: C 955 ASN cc_start: 0.8331 (t0) cc_final: 0.8048 (m-40) outliers start: 53 outliers final: 36 residues processed: 237 average time/residue: 0.3616 time to fit residues: 145.2113 Evaluate side-chains 210 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 173 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 GLN Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 235 ILE 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 754 LEU Chi-restraints excluded: chain B residue 902 MET 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 211 ILE 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 551 VAL Chi-restraints excluded: chain A residue 604 THR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain C residue 66 HIS 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 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 732 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 196 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 158 optimal weight: 0.0770 chunk 277 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 290 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 106 optimal weight: 0.0060 overall best weight: 0.7556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS A 804 GLN A 935 GLN C 66 HIS C 625 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.181841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158063 restraints weight = 34369.410| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 2.39 r_work: 0.3473 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2155 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= 0.126 Angle : 0.590 11.715 37571 Z= 0.291 Chirality : 0.045 0.406 4414 Planarity : 0.004 0.053 4713 Dihedral : 6.803 91.523 5020 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.96 % Favored : 93.98 % Rotamer: Outliers : 1.84 % Allowed : 14.38 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3254 helix: 1.21 (0.20), residues: 707 sheet: 0.41 (0.20), residues: 661 loop : -1.66 (0.13), residues: 1886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 64 HIS 0.015 0.001 HIS C 66 PHE 0.025 0.001 PHE B 133 TYR 0.018 0.001 TYR B 453 ARG 0.004 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00423 ( 43) link_NAG-ASN : angle 2.41372 ( 129) link_BETA1-4 : bond 0.00503 ( 26) link_BETA1-4 : angle 1.84664 ( 78) hydrogen bonds : bond 0.05514 ( 918) hydrogen bonds : angle 4.94539 ( 2514) SS BOND : bond 0.00269 ( 39) SS BOND : angle 1.09530 ( 78) covalent geometry : bond 0.00292 (27419) covalent geometry : angle 0.56647 (37286) Misc. bond : bond 0.00052 ( 3) *********************** 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: 53 poor density : 186 time to evaluate : 2.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8732 (mm) cc_final: 0.8293 (mt) REVERT: B 335 LEU cc_start: 0.8818 (mm) cc_final: 0.8170 (tt) REVERT: B 886 TRP cc_start: 0.8851 (p90) cc_final: 0.8420 (p90) REVERT: B 965 GLN cc_start: 0.8651 (tt0) cc_final: 0.8407 (tp40) REVERT: B 981 PHE cc_start: 0.6671 (m-10) cc_final: 0.6432 (m-10) REVERT: A 569 ILE cc_start: 0.8860 (tp) cc_final: 0.8629 (tt) REVERT: A 673 SER cc_start: 0.8826 (t) cc_final: 0.8599 (p) REVERT: A 779 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8236 (tm-30) REVERT: A 814 LYS cc_start: 0.7602 (mmtt) cc_final: 0.7254 (mmtm) REVERT: A 886 TRP cc_start: 0.8368 (p90) cc_final: 0.8011 (p90) REVERT: C 752 LEU cc_start: 0.8720 (tt) cc_final: 0.8329 (mt) REVERT: C 955 ASN cc_start: 0.8358 (t0) cc_final: 0.8006 (m110) outliers start: 53 outliers final: 34 residues processed: 230 average time/residue: 0.3576 time to fit residues: 139.6866 Evaluate side-chains 212 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 2.856 ------------------------------------------------------------------------------- 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 212 VAL 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 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 193 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 229 VAL 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 911 VAL Chi-restraints excluded: chain A residue 915 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 303 LEU Chi-restraints excluded: chain C residue 538 CYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 126 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 163 optimal weight: 0.4980 chunk 245 optimal weight: 3.9990 chunk 170 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN A 66 HIS C 66 HIS C 207 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 = 0.4118 r_free = 0.4118 target = 0.182033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.143537 restraints weight = 34358.972| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 4.35 r_work (final): 0.3663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27530 Z= 0.122 Angle : 0.581 11.608 37571 Z= 0.286 Chirality : 0.045 0.397 4414 Planarity : 0.004 0.051 4713 Dihedral : 6.324 90.655 5013 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.84 % Favored : 94.10 % Rotamer: Outliers : 2.19 % Allowed : 14.83 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3254 helix: 1.32 (0.20), residues: 705 sheet: 0.49 (0.20), residues: 658 loop : -1.62 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 64 HIS 0.008 0.001 HIS B 207 PHE 0.018 0.001 PHE B 168 TYR 0.018 0.001 TYR B 170 ARG 0.006 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00408 ( 43) link_NAG-ASN : angle 2.39813 ( 129) link_BETA1-4 : bond 0.00496 ( 26) link_BETA1-4 : angle 1.77172 ( 78) hydrogen bonds : bond 0.05343 ( 918) hydrogen bonds : angle 4.87213 ( 2514) SS BOND : bond 0.00256 ( 39) SS BOND : angle 1.14515 ( 78) covalent geometry : bond 0.00282 (27419) covalent geometry : angle 0.55769 (37286) Misc. bond : bond 0.00027 ( 3) *********************** 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 250 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 187 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8736 (mm) cc_final: 0.8386 (mt) REVERT: B 214 GLU cc_start: 0.4228 (OUTLIER) cc_final: 0.4021 (pt0) REVERT: B 402 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7700 (pt) REVERT: B 886 TRP cc_start: 0.8746 (p90) cc_final: 0.8434 (p90) REVERT: A 673 SER cc_start: 0.8590 (t) cc_final: 0.8256 (p) REVERT: A 814 LYS cc_start: 0.7643 (mmtt) cc_final: 0.7248 (mmtm) REVERT: A 886 TRP cc_start: 0.7898 (p90) cc_final: 0.7436 (p90) REVERT: C 752 LEU cc_start: 0.8765 (tt) cc_final: 0.8397 (mt) outliers start: 63 outliers final: 43 residues processed: 240 average time/residue: 0.3596 time to fit residues: 147.7734 Evaluate side-chains 219 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 3.161 ------------------------------------------------------------------------------- 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 214 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 402 ILE 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 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 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 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 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 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 218 LEU Chi-restraints excluded: chain C residue 229 VAL Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 538 CYS Chi-restraints excluded: chain C residue 549 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 326 optimal weight: 6.9990 chunk 199 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 261 optimal weight: 30.0000 chunk 117 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 GLN B 450 ASN B1101 HIS B1119 ASN A 66 HIS A 935 GLN C 66 HIS C 137 ASN C 207 HIS C 955 ASN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.178066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.154720 restraints weight = 34374.143| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.33 r_work: 0.3447 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 27530 Z= 0.215 Angle : 0.662 11.740 37571 Z= 0.330 Chirality : 0.048 0.413 4414 Planarity : 0.004 0.053 4713 Dihedral : 6.379 90.614 5013 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.64 % Favored : 93.30 % Rotamer: Outliers : 2.60 % Allowed : 15.28 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3254 helix: 1.02 (0.20), residues: 712 sheet: 0.30 (0.20), residues: 662 loop : -1.71 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 64 HIS 0.024 0.002 HIS C 66 PHE 0.023 0.002 PHE C 86 TYR 0.020 0.002 TYR A1067 ARG 0.006 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00400 ( 43) link_NAG-ASN : angle 2.58965 ( 129) link_BETA1-4 : bond 0.00476 ( 26) link_BETA1-4 : angle 1.75457 ( 78) hydrogen bonds : bond 0.06939 ( 918) hydrogen bonds : angle 5.10823 ( 2514) SS BOND : bond 0.00380 ( 39) SS BOND : angle 1.47970 ( 78) covalent geometry : bond 0.00543 (27419) covalent geometry : angle 0.63855 (37286) Misc. bond : bond 0.00037 ( 3) *********************** 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 245 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 170 time to evaluate : 2.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 170 TYR cc_start: 0.6613 (t80) cc_final: 0.6359 (t80) REVERT: A 351 TYR cc_start: 0.8572 (p90) cc_final: 0.8250 (p90) REVERT: A 673 SER cc_start: 0.8753 (t) cc_final: 0.8533 (p) REVERT: A 779 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8562 (tm-30) REVERT: A 814 LYS cc_start: 0.7593 (mmtt) cc_final: 0.7261 (mmtm) REVERT: C 218 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7689 (mt) REVERT: C 321 GLN cc_start: 0.5829 (OUTLIER) cc_final: 0.5528 (pt0) outliers start: 75 outliers final: 53 residues processed: 238 average time/residue: 0.3143 time to fit residues: 127.0125 Evaluate side-chains 218 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 163 time to evaluate : 2.602 ------------------------------------------------------------------------------- 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 740 MET 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 B residue 1104 VAL 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 242 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 347 PHE 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 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 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 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 321 GLN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 538 CYS 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 887 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 206 optimal weight: 0.4980 chunk 101 optimal weight: 0.9990 chunk 198 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 230 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 321 optimal weight: 0.8980 chunk 213 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS C 207 HIS C 314 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.180745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156578 restraints weight = 34358.361| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.42 r_work: 0.3459 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2693 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= 0.129 Angle : 0.593 11.382 37571 Z= 0.293 Chirality : 0.045 0.393 4414 Planarity : 0.004 0.052 4713 Dihedral : 6.110 90.711 5013 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.29 % Favored : 94.65 % Rotamer: Outliers : 2.12 % Allowed : 16.22 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3254 helix: 1.25 (0.20), residues: 706 sheet: 0.26 (0.20), residues: 683 loop : -1.64 (0.13), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 633 HIS 0.009 0.001 HIS B 207 PHE 0.016 0.001 PHE B 168 TYR 0.019 0.001 TYR B 453 ARG 0.007 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 43) link_NAG-ASN : angle 2.41333 ( 129) link_BETA1-4 : bond 0.00501 ( 26) link_BETA1-4 : angle 1.75803 ( 78) hydrogen bonds : bond 0.05640 ( 918) hydrogen bonds : angle 4.90993 ( 2514) SS BOND : bond 0.00274 ( 39) SS BOND : angle 1.21383 ( 78) covalent geometry : bond 0.00300 (27419) covalent geometry : angle 0.56967 (37286) Misc. bond : bond 0.00040 ( 3) *********************** 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 240 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 179 time to evaluate : 2.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8651 (mm) cc_final: 0.8210 (mt) REVERT: A 317 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7877 (m-40) REVERT: A 428 ASP cc_start: 0.8364 (p0) cc_final: 0.8162 (p0) REVERT: A 673 SER cc_start: 0.8662 (t) cc_final: 0.8440 (p) REVERT: A 779 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 814 LYS cc_start: 0.7535 (mmtt) cc_final: 0.7198 (mmtm) REVERT: C 200 TYR cc_start: 0.8271 (m-10) cc_final: 0.7887 (m-80) REVERT: C 321 GLN cc_start: 0.5743 (OUTLIER) cc_final: 0.5412 (pt0) REVERT: C 569 ILE cc_start: 0.7836 (OUTLIER) cc_final: 0.7318 (mp) outliers start: 61 outliers final: 41 residues processed: 234 average time/residue: 0.3226 time to fit residues: 128.7331 Evaluate side-chains 211 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 2.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 212 VAL 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 754 LEU Chi-restraints excluded: chain B residue 902 MET 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 274 THR Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 347 PHE 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 909 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 274 THR 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 538 CYS 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 887 THR Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 164 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 191 optimal weight: 0.8980 chunk 261 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 137 optimal weight: 0.6980 chunk 142 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS C 207 HIS C 580 GLN ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.181024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156429 restraints weight = 34074.173| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.41 r_work: 0.3461 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27530 Z= 0.125 Angle : 0.585 11.186 37571 Z= 0.288 Chirality : 0.045 0.388 4414 Planarity : 0.004 0.052 4713 Dihedral : 5.891 89.624 5010 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 2.15 % Allowed : 16.74 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3254 helix: 1.33 (0.20), residues: 706 sheet: 0.32 (0.20), residues: 685 loop : -1.59 (0.13), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 64 HIS 0.011 0.001 HIS B 207 PHE 0.025 0.001 PHE B 133 TYR 0.020 0.001 TYR B 170 ARG 0.007 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00403 ( 43) link_NAG-ASN : angle 2.37666 ( 129) link_BETA1-4 : bond 0.00488 ( 26) link_BETA1-4 : angle 1.72704 ( 78) hydrogen bonds : bond 0.05450 ( 918) hydrogen bonds : angle 4.82259 ( 2514) SS BOND : bond 0.00281 ( 39) SS BOND : angle 1.13779 ( 78) covalent geometry : bond 0.00291 (27419) covalent geometry : angle 0.56210 (37286) Misc. bond : bond 0.00045 ( 3) *********************** 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 236 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 174 time to evaluate : 2.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8684 (mm) cc_final: 0.8254 (mt) REVERT: B 170 TYR cc_start: 0.6705 (t80) cc_final: 0.6494 (t80) REVERT: B 335 LEU cc_start: 0.8723 (mm) cc_final: 0.8103 (tt) REVERT: A 317 ASN cc_start: 0.8145 (OUTLIER) cc_final: 0.7857 (m-40) REVERT: A 351 TYR cc_start: 0.8513 (p90) cc_final: 0.8234 (p90) REVERT: A 673 SER cc_start: 0.8683 (t) cc_final: 0.8466 (p) REVERT: A 814 LYS cc_start: 0.7536 (mmtt) cc_final: 0.7188 (mmtm) REVERT: C 200 TYR cc_start: 0.8236 (m-10) cc_final: 0.7879 (m-80) REVERT: C 321 GLN cc_start: 0.5675 (OUTLIER) cc_final: 0.5270 (pt0) REVERT: C 569 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7327 (mp) outliers start: 62 outliers final: 49 residues processed: 230 average time/residue: 0.3485 time to fit residues: 136.7330 Evaluate side-chains 221 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 169 time to evaluate : 3.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 212 VAL 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 573 THR 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 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 101 ILE 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 233 ILE 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 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 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 274 THR 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 538 CYS 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 887 THR Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 283 optimal weight: 1.9990 chunk 225 optimal weight: 4.9990 chunk 275 optimal weight: 0.1980 chunk 276 optimal weight: 0.0370 chunk 170 optimal weight: 0.9980 chunk 229 optimal weight: 1.9990 chunk 267 optimal weight: 4.9990 chunk 308 optimal weight: 0.0870 chunk 299 optimal weight: 0.6980 chunk 292 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN A 66 HIS C 207 HIS C 580 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 = 0.4130 r_free = 0.4130 target = 0.183300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156310 restraints weight = 34202.864| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 2.67 r_work: 0.3435 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27530 Z= 0.104 Angle : 0.559 10.948 37571 Z= 0.275 Chirality : 0.044 0.373 4414 Planarity : 0.004 0.052 4713 Dihedral : 5.591 87.585 5010 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.01 % Favored : 94.93 % Rotamer: Outliers : 1.84 % Allowed : 17.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.15), residues: 3254 helix: 1.54 (0.20), residues: 709 sheet: 0.38 (0.20), residues: 698 loop : -1.53 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.012 0.001 HIS B 207 PHE 0.015 0.001 PHE B 168 TYR 0.020 0.001 TYR B 170 ARG 0.007 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 43) link_NAG-ASN : angle 2.29004 ( 129) link_BETA1-4 : bond 0.00507 ( 26) link_BETA1-4 : angle 1.71188 ( 78) hydrogen bonds : bond 0.04641 ( 918) hydrogen bonds : angle 4.63914 ( 2514) SS BOND : bond 0.00245 ( 39) SS BOND : angle 0.86577 ( 78) covalent geometry : bond 0.00229 (27419) covalent geometry : angle 0.53784 (37286) Misc. bond : bond 0.00041 ( 3) *********************** 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 233 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 180 time to evaluate : 3.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8681 (mm) cc_final: 0.8277 (mt) REVERT: B 335 LEU cc_start: 0.8753 (mm) cc_final: 0.8072 (tt) REVERT: A 428 ASP cc_start: 0.8483 (p0) cc_final: 0.8261 (p0) REVERT: A 673 SER cc_start: 0.8767 (t) cc_final: 0.8550 (p) REVERT: C 200 TYR cc_start: 0.8291 (m-10) cc_final: 0.7954 (m-80) REVERT: C 321 GLN cc_start: 0.5499 (OUTLIER) cc_final: 0.5176 (pt0) outliers start: 53 outliers final: 46 residues processed: 225 average time/residue: 0.5732 time to fit residues: 228.0802 Evaluate side-chains 211 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 164 time to evaluate : 3.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 274 THR 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 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 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 127 VAL Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 347 PHE 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 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 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 274 THR 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 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 909 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 133 optimal weight: 0.7980 chunk 14 optimal weight: 8.9990 chunk 156 optimal weight: 0.4980 chunk 26 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 277 optimal weight: 0.8980 chunk 141 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 199 optimal weight: 2.9990 chunk 185 optimal weight: 0.5980 chunk 318 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** C 207 HIS ** 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 = 0.4116 r_free = 0.4116 target = 0.181836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.147733 restraints weight = 34010.225| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.20 r_work: 0.3330 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 27530 Z= 0.123 Angle : 0.575 10.932 37571 Z= 0.283 Chirality : 0.045 0.379 4414 Planarity : 0.004 0.052 4713 Dihedral : 5.551 85.502 5010 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.99 % Favored : 93.95 % Rotamer: Outliers : 1.77 % Allowed : 17.60 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.15), residues: 3254 helix: 1.48 (0.20), residues: 715 sheet: 0.41 (0.20), residues: 687 loop : -1.55 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.010 0.001 HIS C 207 PHE 0.023 0.001 PHE B 133 TYR 0.020 0.001 TYR B 453 ARG 0.007 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00383 ( 43) link_NAG-ASN : angle 2.31428 ( 129) link_BETA1-4 : bond 0.00497 ( 26) link_BETA1-4 : angle 1.70037 ( 78) hydrogen bonds : bond 0.05126 ( 918) hydrogen bonds : angle 4.67070 ( 2514) SS BOND : bond 0.00247 ( 39) SS BOND : angle 1.07718 ( 78) covalent geometry : bond 0.00290 (27419) covalent geometry : angle 0.55310 (37286) Misc. bond : bond 0.00023 ( 3) ********************** 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 220 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 128 ILE cc_start: 0.8723 (mm) cc_final: 0.8309 (mt) REVERT: B 335 LEU cc_start: 0.8842 (mm) cc_final: 0.8091 (tt) REVERT: A 317 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7954 (m-40) REVERT: A 428 ASP cc_start: 0.8542 (p0) cc_final: 0.8327 (p0) REVERT: A 558 LYS cc_start: 0.8454 (tttm) cc_final: 0.8218 (ttpt) REVERT: A 673 SER cc_start: 0.8806 (t) cc_final: 0.8590 (p) REVERT: A 814 LYS cc_start: 0.7721 (mmtt) cc_final: 0.7330 (mmtm) REVERT: C 200 TYR cc_start: 0.8364 (m-10) cc_final: 0.8017 (m-80) REVERT: C 321 GLN cc_start: 0.5447 (OUTLIER) cc_final: 0.5091 (pt0) outliers start: 51 outliers final: 45 residues processed: 213 average time/residue: 0.3274 time to fit residues: 118.6619 Evaluate side-chains 212 residues out of total 2886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 165 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 274 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 740 MET Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 902 MET 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 233 ILE 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 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 620 VAL Chi-restraints excluded: chain A residue 723 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 1122 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 274 THR 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 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 909 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 256 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 261 optimal weight: 20.0000 chunk 302 optimal weight: 0.2980 chunk 158 optimal weight: 0.1980 chunk 268 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS ** B 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** C 207 HIS ** 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 = 0.4121 r_free = 0.4121 target = 0.182398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.157756 restraints weight = 34189.851| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.43 r_work: 0.3472 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27530 Z= 0.116 Angle : 0.569 10.928 37571 Z= 0.280 Chirality : 0.044 0.386 4414 Planarity : 0.004 0.052 4713 Dihedral : 5.468 83.360 5010 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.29 % Favored : 94.65 % Rotamer: Outliers : 1.84 % Allowed : 17.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.15), residues: 3254 helix: 1.57 (0.20), residues: 709 sheet: 0.46 (0.20), residues: 677 loop : -1.54 (0.14), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 633 HIS 0.013 0.001 HIS B 207 PHE 0.024 0.001 PHE B 133 TYR 0.020 0.001 TYR B 453 ARG 0.007 0.000 ARG A 498 Details of bonding type rmsd link_NAG-ASN : bond 0.00399 ( 43) link_NAG-ASN : angle 2.29091 ( 129) link_BETA1-4 : bond 0.00492 ( 26) link_BETA1-4 : angle 1.70536 ( 78) hydrogen bonds : bond 0.04978 ( 918) hydrogen bonds : angle 4.63704 ( 2514) SS BOND : bond 0.00245 ( 39) SS BOND : angle 0.98899 ( 78) covalent geometry : bond 0.00268 (27419) covalent geometry : angle 0.54779 (37286) Misc. bond : bond 0.00020 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11563.22 seconds wall clock time: 207 minutes 2.71 seconds (12422.71 seconds total)