Starting phenix.real_space_refine on Mon Jun 23 04:02:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xns_33325/06_2025/7xns_33325.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xns_33325/06_2025/7xns_33325.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xns_33325/06_2025/7xns_33325.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xns_33325/06_2025/7xns_33325.map" model { file = "/net/cci-nas-00/data/ceres_data/7xns_33325/06_2025/7xns_33325.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xns_33325/06_2025/7xns_33325.cif" } resolution = 3.48 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= -0.000 sd= 0.060 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 114 5.16 5 C 16941 2.51 5 N 4341 2.21 5 O 5199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26595 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8557 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8557 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 8557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8557 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 17.06, per 1000 atoms: 0.64 Number of scatterers: 26595 At special positions: 0 Unit cell: (154.08, 153.01, 181.9, 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 114 16.00 O 5199 8.00 N 4341 7.00 C 16941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 165 " " NAG A1308 " - " ASN A 234 " " NAG A1309 " - " ASN A 331 " " NAG A1310 " - " ASN A 343 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 603 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 165 " " NAG B1308 " - " ASN B 234 " " NAG B1309 " - " ASN B 331 " " NAG B1310 " - " ASN B 343 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 603 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 165 " " NAG C1308 " - " ASN C 234 " " NAG C1309 " - " ASN C 331 " " NAG C1310 " - " ASN C 343 " " NAG D 1 " - " ASN A 616 " " NAG E 1 " - " ASN A 709 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 616 " " NAG K 1 " - " ASN B 709 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 616 " " NAG Q 1 " - " ASN C 709 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 7.22 Conformation dependent library (CDL) restraints added in 3.4 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6144 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 45 sheets defined 23.1% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.77 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.911A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.573A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.582A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.621A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.999A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.612A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 removed outlier: 4.175A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 780 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.617A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.247A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.645A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.720A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.081A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.335A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER A1021 " --> pdb=" O GLU A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1150 removed outlier: 4.169A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS A1149 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A1150 " --> pdb=" O ASP A1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.908A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN B 343 " --> pdb=" O ASP B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.686A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.583A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.661A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.568A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 757 removed outlier: 3.728A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 removed outlier: 4.125A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.816A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.286A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.607A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.703A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N SER B 939 " --> pdb=" O GLN B 935 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.149A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.218A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1150 removed outlier: 4.160A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS B1149 " --> pdb=" O LEU B1145 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU B1150 " --> pdb=" O ASP B1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.903A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN C 343 " --> pdb=" O ASP C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.528A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.595A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.579A pdb=" N TYR C 421 " --> pdb=" O ASN C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 619 through 624 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.947A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 757 removed outlier: 3.728A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 4.230A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.642A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.290A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.630A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.730A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 938 " --> pdb=" O ILE C 934 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.121A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.352A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1150 removed outlier: 4.030A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C1149 " --> pdb=" O LEU C1145 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU C1150 " --> pdb=" O ASP C1146 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.879A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.511A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 172 removed outlier: 3.809A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.341A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.748A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.627A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.257A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.839A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 567 through 568 removed outlier: 3.964A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.650A pdb=" N GLU A 654 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 694 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.111A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.910A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.512A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.901A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.360A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.826A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.573A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.282A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.826A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 567 through 568 removed outlier: 3.965A pdb=" N THR B 572 " --> pdb=" O ASP B 568 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.617A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 712 through 715 Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.055A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD4, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.896A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.970A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 169 through 172 removed outlier: 3.860A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.338A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.803A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 576 " --> pdb=" O LEU C 585 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.628A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.244A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.836A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 567 through 568 removed outlier: 3.951A pdb=" N THR C 572 " --> pdb=" O ASP C 568 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.046A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 715 Processing sheet with id=AE7, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.111A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1096 833 hydrogen bonds defined for protein. 2298 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: 11.58 Time building geometry restraints manager: 8.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8418 1.34 - 1.46: 6742 1.46 - 1.58: 11921 1.58 - 1.70: 0 1.70 - 1.83: 144 Bond restraints: 27225 Sorted by residual: bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.42e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C1 NAG B1310 " pdb=" O5 NAG B1310 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" C1 NAG C1310 " pdb=" O5 NAG C1310 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.59e+00 ... (remaining 27220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 35508 1.49 - 2.99: 1379 2.99 - 4.48: 147 4.48 - 5.98: 32 5.98 - 7.47: 11 Bond angle restraints: 37077 Sorted by residual: angle pdb=" C THR A 333 " pdb=" N ASN A 334 " pdb=" CA ASN A 334 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 angle pdb=" C THR B 333 " pdb=" N ASN B 334 " pdb=" CA ASN B 334 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.51e+01 angle pdb=" C THR C 333 " pdb=" N ASN C 334 " pdb=" CA ASN C 334 " ideal model delta sigma weight residual 121.54 128.89 -7.35 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N ASP B1041 " pdb=" CA ASP B1041 " pdb=" CB ASP B1041 " ideal model delta sigma weight residual 113.15 108.25 4.90 1.63e+00 3.76e-01 9.05e+00 angle pdb=" CA ASP B1041 " pdb=" CB ASP B1041 " pdb=" CG ASP B1041 " ideal model delta sigma weight residual 112.60 115.58 -2.98 1.00e+00 1.00e+00 8.89e+00 ... (remaining 37072 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.15: 15933 23.15 - 46.30: 894 46.30 - 69.45: 116 69.45 - 92.60: 40 92.60 - 115.75: 48 Dihedral angle restraints: 17031 sinusoidal: 7464 harmonic: 9567 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -154.73 68.73 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -154.64 68.64 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -154.26 68.26 1 1.00e+01 1.00e-02 6.04e+01 ... (remaining 17028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3901 0.082 - 0.164: 443 0.164 - 0.246: 15 0.246 - 0.328: 0 0.328 - 0.410: 6 Chirality restraints: 4365 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN A1134 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.15e+00 ... (remaining 4362 not shown) Planarity restraints: 4770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A1041 " 0.012 2.00e-02 2.50e+03 2.31e-02 5.32e+00 pdb=" C ASP A1041 " -0.040 2.00e-02 2.50e+03 pdb=" O ASP A1041 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE A1042 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 229 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO C 230 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 230 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 230 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 229 " 0.035 5.00e-02 4.00e+02 5.30e-02 4.49e+00 pdb=" N PRO A 230 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.029 5.00e-02 4.00e+02 ... (remaining 4767 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5858 2.78 - 3.31: 24187 3.31 - 3.84: 40275 3.84 - 4.37: 45339 4.37 - 4.90: 79900 Nonbonded interactions: 195559 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" OD2 ASP B 53 " model vdw 2.252 3.040 nonbonded pdb=" NE2 HIS B 66 " pdb=" OG1 THR B 250 " model vdw 2.285 3.120 nonbonded pdb=" NZ LYS A 825 " pdb=" O LEU A 938 " model vdw 2.287 3.120 nonbonded pdb=" NZ LYS B 825 " pdb=" O LEU B 938 " model vdw 2.290 3.120 nonbonded pdb=" NE2 HIS A 66 " pdb=" OG1 THR A 250 " model vdw 2.291 3.120 ... (remaining 195554 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 1.550 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: 0.040 Extract box with map and model: 1.050 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 63.800 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 27327 Z= 0.203 Angle : 0.678 9.419 37347 Z= 0.344 Chirality : 0.049 0.410 4365 Planarity : 0.004 0.055 4722 Dihedral : 15.419 115.752 10779 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.65 (0.15), residues: 3267 helix: 1.59 (0.22), residues: 687 sheet: -0.14 (0.20), residues: 666 loop : -1.35 (0.14), residues: 1914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 104 HIS 0.005 0.001 HIS C 245 PHE 0.029 0.002 PHE A 906 TYR 0.017 0.001 TYR B1067 ARG 0.009 0.001 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 48) link_NAG-ASN : angle 2.76149 ( 144) link_BETA1-4 : bond 0.00524 ( 18) link_BETA1-4 : angle 1.98728 ( 54) hydrogen bonds : bond 0.15487 ( 833) hydrogen bonds : angle 6.11735 ( 2298) SS BOND : bond 0.00208 ( 36) SS BOND : angle 1.13289 ( 72) covalent geometry : bond 0.00432 (27225) covalent geometry : angle 0.65226 (37077) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 2.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2509 (mmp) cc_final: 0.1551 (mpp) REVERT: A 869 MET cc_start: 0.8159 (mtp) cc_final: 0.7799 (mtt) REVERT: A 902 MET cc_start: 0.8143 (tpt) cc_final: 0.7841 (mmt) REVERT: B 153 MET cc_start: 0.2070 (mmp) cc_final: 0.1277 (mpp) REVERT: B 965 GLN cc_start: 0.8490 (tm-30) cc_final: 0.7931 (tm-30) REVERT: B 988 GLU cc_start: 0.7262 (mp0) cc_final: 0.7037 (mp0) REVERT: C 153 MET cc_start: 0.2405 (mmp) cc_final: 0.1673 (mpp) REVERT: C 175 PHE cc_start: 0.7579 (m-80) cc_final: 0.7331 (m-80) REVERT: C 508 TYR cc_start: 0.6671 (m-80) cc_final: 0.6348 (m-80) REVERT: C 1130 ILE cc_start: 0.8047 (mp) cc_final: 0.7787 (mt) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.4255 time to fit residues: 236.4542 Evaluate side-chains 202 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 4.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 276 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 167 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 256 optimal weight: 0.0870 chunk 99 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 190 optimal weight: 0.0570 chunk 296 optimal weight: 3.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1119 ASN B 148 ASN B 207 HIS C 148 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.188616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.133392 restraints weight = 40101.694| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.52 r_work: 0.3460 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27327 Z= 0.117 Angle : 0.628 12.930 37347 Z= 0.304 Chirality : 0.046 0.325 4365 Planarity : 0.005 0.059 4722 Dihedral : 11.725 109.848 4914 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.88 % Allowed : 5.92 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3267 helix: 1.51 (0.21), residues: 711 sheet: -0.18 (0.20), residues: 681 loop : -1.36 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.003 0.001 HIS C 245 PHE 0.024 0.001 PHE B 175 TYR 0.020 0.001 TYR B 269 ARG 0.010 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00746 ( 48) link_NAG-ASN : angle 2.99562 ( 144) link_BETA1-4 : bond 0.00402 ( 18) link_BETA1-4 : angle 1.90384 ( 54) hydrogen bonds : bond 0.04786 ( 833) hydrogen bonds : angle 5.05012 ( 2298) SS BOND : bond 0.00153 ( 36) SS BOND : angle 0.90043 ( 72) covalent geometry : bond 0.00249 (27225) covalent geometry : angle 0.59576 (37077) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 229 time to evaluate : 2.910 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.2495 (mmp) cc_final: 0.1919 (mpp) REVERT: A 564 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.7045 (pt0) REVERT: B 153 MET cc_start: 0.2176 (mmp) cc_final: 0.1327 (mpp) REVERT: B 200 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.6525 (t80) REVERT: B 229 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7250 (mt) REVERT: B 965 GLN cc_start: 0.8543 (tm-30) cc_final: 0.7920 (tm-30) REVERT: C 153 MET cc_start: 0.2570 (mmt) cc_final: 0.1898 (mpp) REVERT: C 382 VAL cc_start: 0.7649 (t) cc_final: 0.7414 (t) REVERT: C 508 TYR cc_start: 0.5903 (m-80) cc_final: 0.5632 (m-80) REVERT: C 754 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8634 (tt) REVERT: C 1130 ILE cc_start: 0.7956 (mp) cc_final: 0.7677 (mt) outliers start: 25 outliers final: 14 residues processed: 240 average time/residue: 0.3378 time to fit residues: 136.1349 Evaluate side-chains 217 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 2.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1117 THR Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 991 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 319 optimal weight: 0.6980 chunk 13 optimal weight: 30.0000 chunk 101 optimal weight: 1.9990 chunk 251 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 186 optimal weight: 0.6980 chunk 275 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 165 optimal weight: 0.0010 chunk 118 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 613 GLN C 613 GLN C 658 ASN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.185361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.128244 restraints weight = 40397.020| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.10 r_work: 0.3400 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27327 Z= 0.142 Angle : 0.635 12.498 37347 Z= 0.304 Chirality : 0.047 0.314 4365 Planarity : 0.004 0.052 4722 Dihedral : 10.477 110.652 4914 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.79 % Allowed : 8.72 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3267 helix: 1.83 (0.22), residues: 663 sheet: -0.12 (0.20), residues: 648 loop : -1.41 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 104 HIS 0.003 0.001 HIS C1088 PHE 0.024 0.002 PHE C 175 TYR 0.020 0.001 TYR B1067 ARG 0.007 0.000 ARG A1107 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 48) link_NAG-ASN : angle 2.78508 ( 144) link_BETA1-4 : bond 0.00361 ( 18) link_BETA1-4 : angle 2.00481 ( 54) hydrogen bonds : bond 0.04843 ( 833) hydrogen bonds : angle 4.88697 ( 2298) SS BOND : bond 0.00161 ( 36) SS BOND : angle 0.93264 ( 72) covalent geometry : bond 0.00336 (27225) covalent geometry : angle 0.60707 (37077) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 3.512 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2522 (mmp) cc_final: 0.1890 (mpp) REVERT: B 153 MET cc_start: 0.2096 (mmp) cc_final: 0.1343 (mpp) REVERT: B 965 GLN cc_start: 0.8610 (tm-30) cc_final: 0.7950 (tm-30) REVERT: C 153 MET cc_start: 0.2616 (mmt) cc_final: 0.1982 (mpp) REVERT: C 382 VAL cc_start: 0.8107 (t) cc_final: 0.7874 (m) REVERT: C 515 PHE cc_start: 0.7817 (m-80) cc_final: 0.7455 (m-10) REVERT: C 752 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9212 (tt) REVERT: C 1130 ILE cc_start: 0.8096 (mp) cc_final: 0.7789 (mt) outliers start: 51 outliers final: 28 residues processed: 243 average time/residue: 0.5572 time to fit residues: 227.5340 Evaluate side-chains 220 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 3.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 136 optimal weight: 0.5980 chunk 326 optimal weight: 0.0970 chunk 297 optimal weight: 9.9990 chunk 316 optimal weight: 4.9990 chunk 262 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 246 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 272 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 GLN B 658 ASN B 957 GLN C 658 ASN ** C 957 GLN ** 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 = 0.4323 r_free = 0.4323 target = 0.177604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.125426 restraints weight = 40398.851| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.71 r_work: 0.3412 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 27327 Z= 0.187 Angle : 0.662 9.478 37347 Z= 0.321 Chirality : 0.049 0.345 4365 Planarity : 0.005 0.055 4722 Dihedral : 9.015 109.170 4914 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.42 % Allowed : 10.71 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.14), residues: 3267 helix: 1.60 (0.22), residues: 666 sheet: -0.23 (0.20), residues: 642 loop : -1.48 (0.13), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 64 HIS 0.005 0.001 HIS C 66 PHE 0.021 0.002 PHE B1121 TYR 0.021 0.001 TYR B1067 ARG 0.006 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00520 ( 48) link_NAG-ASN : angle 2.82887 ( 144) link_BETA1-4 : bond 0.00451 ( 18) link_BETA1-4 : angle 2.61162 ( 54) hydrogen bonds : bond 0.05567 ( 833) hydrogen bonds : angle 4.98624 ( 2298) SS BOND : bond 0.00251 ( 36) SS BOND : angle 1.06700 ( 72) covalent geometry : bond 0.00453 (27225) covalent geometry : angle 0.63111 (37077) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 209 time to evaluate : 2.852 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.1815 (mmt) cc_final: 0.1194 (mpp) REVERT: A 177 MET cc_start: 0.7702 (ppp) cc_final: 0.7285 (ppp) REVERT: B 153 MET cc_start: 0.1977 (mmt) cc_final: 0.1448 (mpp) REVERT: B 965 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8023 (tm-30) REVERT: C 153 MET cc_start: 0.2677 (mmt) cc_final: 0.2106 (mpp) REVERT: C 177 MET cc_start: 0.7636 (ppp) cc_final: 0.6886 (mpp) REVERT: C 508 TYR cc_start: 0.6036 (m-80) cc_final: 0.5807 (m-80) REVERT: C 515 PHE cc_start: 0.7918 (m-80) cc_final: 0.7557 (m-10) REVERT: C 574 ASP cc_start: 0.8188 (t0) cc_final: 0.7923 (t0) REVERT: C 752 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9244 (tt) REVERT: C 977 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8303 (mp) REVERT: C 1130 ILE cc_start: 0.8266 (mp) cc_final: 0.7787 (tp) outliers start: 69 outliers final: 47 residues processed: 255 average time/residue: 0.3488 time to fit residues: 152.2011 Evaluate side-chains 238 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 189 time to evaluate : 2.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1118 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 88 optimal weight: 5.9990 chunk 139 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 268 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 226 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 506 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1088 HIS B 439 ASN B 658 ASN B 957 GLN C 506 GLN C 658 ASN ** C 957 GLN ** 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 = 0.4280 r_free = 0.4280 target = 0.173602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123903 restraints weight = 40322.732| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.66 r_work: 0.3357 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 27327 Z= 0.282 Angle : 0.758 10.119 37347 Z= 0.375 Chirality : 0.052 0.390 4365 Planarity : 0.005 0.058 4722 Dihedral : 8.124 105.154 4914 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.22 % Allowed : 12.46 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.14), residues: 3267 helix: 1.43 (0.21), residues: 645 sheet: -0.69 (0.19), residues: 723 loop : -1.68 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 64 HIS 0.006 0.002 HIS B1088 PHE 0.025 0.002 PHE B1121 TYR 0.023 0.002 TYR B1067 ARG 0.004 0.001 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00596 ( 48) link_NAG-ASN : angle 3.06319 ( 144) link_BETA1-4 : bond 0.00338 ( 18) link_BETA1-4 : angle 3.01360 ( 54) hydrogen bonds : bond 0.06668 ( 833) hydrogen bonds : angle 5.35015 ( 2298) SS BOND : bond 0.00286 ( 36) SS BOND : angle 1.93709 ( 72) covalent geometry : bond 0.00699 (27225) covalent geometry : angle 0.72198 (37077) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 203 time to evaluate : 2.717 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.2298 (mmt) cc_final: 0.1653 (mpp) REVERT: A 177 MET cc_start: 0.7791 (ppp) cc_final: 0.7396 (ppp) REVERT: B 153 MET cc_start: 0.2161 (mmt) cc_final: 0.1479 (mpp) REVERT: B 200 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6647 (t80) REVERT: B 266 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7597 (m-10) REVERT: B 388 ASN cc_start: 0.8407 (m-40) cc_final: 0.8158 (t0) REVERT: B 508 TYR cc_start: 0.6374 (m-80) cc_final: 0.6169 (m-80) REVERT: B 661 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7806 (mm-30) REVERT: B 752 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9163 (tt) REVERT: B 965 GLN cc_start: 0.8740 (tm-30) cc_final: 0.8007 (tm-30) REVERT: C 153 MET cc_start: 0.2282 (mmt) cc_final: 0.1783 (mpp) REVERT: C 495 TYR cc_start: 0.6826 (m-80) cc_final: 0.6474 (m-80) REVERT: C 508 TYR cc_start: 0.6303 (m-80) cc_final: 0.6094 (m-80) REVERT: C 515 PHE cc_start: 0.8019 (m-80) cc_final: 0.7721 (m-10) REVERT: C 1130 ILE cc_start: 0.8359 (mp) cc_final: 0.8050 (mt) outliers start: 92 outliers final: 70 residues processed: 270 average time/residue: 0.3239 time to fit residues: 148.9545 Evaluate side-chains 261 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 188 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 64 TRP Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 775 ASP Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 199 optimal weight: 0.7980 chunk 235 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 305 optimal weight: 0.8980 chunk 258 optimal weight: 30.0000 chunk 7 optimal weight: 9.9990 chunk 177 optimal weight: 0.5980 chunk 46 optimal weight: 40.0000 chunk 165 optimal weight: 9.9990 chunk 194 optimal weight: 0.5980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN B 564 GLN B 957 GLN C 658 ASN C 957 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.176653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.3577 r_free = 0.3577 target = 0.118599 restraints weight = 40054.278| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 3.13 r_work: 0.3338 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27327 Z= 0.147 Angle : 0.648 11.161 37347 Z= 0.314 Chirality : 0.048 0.337 4365 Planarity : 0.004 0.056 4722 Dihedral : 7.611 100.481 4914 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.56 % Allowed : 13.27 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3267 helix: 1.59 (0.22), residues: 666 sheet: -0.44 (0.20), residues: 693 loop : -1.63 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 104 HIS 0.004 0.001 HIS A1088 PHE 0.020 0.001 PHE A1121 TYR 0.022 0.001 TYR B1067 ARG 0.004 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00484 ( 48) link_NAG-ASN : angle 2.75593 ( 144) link_BETA1-4 : bond 0.00330 ( 18) link_BETA1-4 : angle 2.63701 ( 54) hydrogen bonds : bond 0.05173 ( 833) hydrogen bonds : angle 4.93808 ( 2298) SS BOND : bond 0.00282 ( 36) SS BOND : angle 1.18263 ( 72) covalent geometry : bond 0.00346 (27225) covalent geometry : angle 0.61644 (37077) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 187 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2242 (mmt) cc_final: 0.1751 (mpp) REVERT: A 177 MET cc_start: 0.7843 (ppp) cc_final: 0.7524 (ppp) REVERT: A 461 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6608 (pp) REVERT: B 153 MET cc_start: 0.2057 (mmt) cc_final: 0.1439 (mpp) REVERT: B 200 TYR cc_start: 0.6935 (OUTLIER) cc_final: 0.6516 (t80) REVERT: B 266 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7189 (m-10) REVERT: B 388 ASN cc_start: 0.8356 (m-40) cc_final: 0.8092 (t0) REVERT: B 461 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6411 (pp) REVERT: B 759 PHE cc_start: 0.7969 (OUTLIER) cc_final: 0.7406 (t80) REVERT: B 965 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7856 (tm-30) REVERT: C 153 MET cc_start: 0.2141 (mmt) cc_final: 0.1821 (mpp) REVERT: C 177 MET cc_start: 0.7723 (ppp) cc_final: 0.7157 (mpp) REVERT: C 515 PHE cc_start: 0.7810 (m-80) cc_final: 0.7439 (m-10) REVERT: C 574 ASP cc_start: 0.8193 (t0) cc_final: 0.7713 (t0) REVERT: C 759 PHE cc_start: 0.7988 (OUTLIER) cc_final: 0.7361 (t80) REVERT: C 762 GLN cc_start: 0.7278 (mp10) cc_final: 0.7054 (mp10) REVERT: C 1130 ILE cc_start: 0.8276 (mp) cc_final: 0.7826 (tp) outliers start: 73 outliers final: 55 residues processed: 244 average time/residue: 0.3218 time to fit residues: 134.3758 Evaluate side-chains 242 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 181 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1097 SER Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 60 optimal weight: 0.2980 chunk 138 optimal weight: 0.9980 chunk 259 optimal weight: 20.0000 chunk 236 optimal weight: 0.0770 chunk 115 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 314 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 193 optimal weight: 0.4980 chunk 136 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN C 658 ASN C1119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.179784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123367 restraints weight = 40391.126| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 3.24 r_work: 0.3380 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 27327 Z= 0.107 Angle : 0.606 11.528 37347 Z= 0.290 Chirality : 0.046 0.317 4365 Planarity : 0.004 0.053 4722 Dihedral : 6.802 91.307 4914 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.89 % Allowed : 14.57 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3267 helix: 2.14 (0.22), residues: 648 sheet: -0.42 (0.20), residues: 687 loop : -1.41 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 104 HIS 0.002 0.000 HIS B1088 PHE 0.016 0.001 PHE A 175 TYR 0.018 0.001 TYR B1067 ARG 0.004 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 48) link_NAG-ASN : angle 2.68125 ( 144) link_BETA1-4 : bond 0.00389 ( 18) link_BETA1-4 : angle 2.27994 ( 54) hydrogen bonds : bond 0.03990 ( 833) hydrogen bonds : angle 4.54086 ( 2298) SS BOND : bond 0.00208 ( 36) SS BOND : angle 0.80412 ( 72) covalent geometry : bond 0.00237 (27225) covalent geometry : angle 0.57735 (37077) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 202 time to evaluate : 2.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1656 (mmt) cc_final: 0.0862 (mpp) REVERT: A 177 MET cc_start: 0.7879 (ppp) cc_final: 0.7540 (ppp) REVERT: A 347 PHE cc_start: 0.5914 (OUTLIER) cc_final: 0.4898 (t80) REVERT: A 461 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6518 (pp) REVERT: A 1002 GLN cc_start: 0.8174 (tt0) cc_final: 0.7807 (tt0) REVERT: B 128 ILE cc_start: 0.8459 (mp) cc_final: 0.8250 (mt) REVERT: B 153 MET cc_start: 0.1853 (mmt) cc_final: 0.1313 (mpp) REVERT: B 200 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6498 (t80) REVERT: B 388 ASN cc_start: 0.8282 (m-40) cc_final: 0.8029 (t0) REVERT: B 461 LEU cc_start: 0.6849 (OUTLIER) cc_final: 0.6510 (pp) REVERT: B 752 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9131 (tt) REVERT: B 759 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.7313 (t80) REVERT: B 965 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7641 (tm-30) REVERT: C 153 MET cc_start: 0.2267 (mmt) cc_final: 0.2016 (mpp) REVERT: C 177 MET cc_start: 0.7719 (ppp) cc_final: 0.7158 (mpp) REVERT: C 515 PHE cc_start: 0.7864 (m-80) cc_final: 0.7552 (m-10) REVERT: C 574 ASP cc_start: 0.8075 (t0) cc_final: 0.7594 (t0) REVERT: C 752 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9187 (tt) REVERT: C 759 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7248 (t80) REVERT: C 1130 ILE cc_start: 0.8196 (mp) cc_final: 0.7787 (tp) outliers start: 54 outliers final: 39 residues processed: 243 average time/residue: 0.3325 time to fit residues: 137.5958 Evaluate side-chains 230 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 183 time to evaluate : 2.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 144 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 299 optimal weight: 0.8980 chunk 122 optimal weight: 30.0000 chunk 278 optimal weight: 0.0070 chunk 247 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 300 optimal weight: 0.6980 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.178256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.125808 restraints weight = 40274.444| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.75 r_work: 0.3429 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27327 Z= 0.127 Angle : 0.609 11.714 37347 Z= 0.294 Chirality : 0.046 0.320 4365 Planarity : 0.004 0.053 4722 Dihedral : 6.463 83.656 4914 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.28 % Allowed : 14.67 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 3267 helix: 2.13 (0.22), residues: 651 sheet: -0.52 (0.19), residues: 708 loop : -1.37 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 64 HIS 0.003 0.001 HIS A1088 PHE 0.018 0.001 PHE A1121 TYR 0.018 0.001 TYR B1067 ARG 0.003 0.000 ARG C 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00472 ( 48) link_NAG-ASN : angle 2.81368 ( 144) link_BETA1-4 : bond 0.00340 ( 18) link_BETA1-4 : angle 1.96076 ( 54) hydrogen bonds : bond 0.04385 ( 833) hydrogen bonds : angle 4.54219 ( 2298) SS BOND : bond 0.00187 ( 36) SS BOND : angle 0.86417 ( 72) covalent geometry : bond 0.00298 (27225) covalent geometry : angle 0.57984 (37077) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 193 time to evaluate : 2.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1994 (mmt) cc_final: 0.1220 (mpp) REVERT: A 177 MET cc_start: 0.7730 (ppp) cc_final: 0.7416 (ppp) REVERT: A 461 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6535 (pp) REVERT: B 128 ILE cc_start: 0.8489 (mp) cc_final: 0.8237 (mt) REVERT: B 153 MET cc_start: 0.1844 (mmt) cc_final: 0.1355 (mpp) REVERT: B 200 TYR cc_start: 0.6971 (OUTLIER) cc_final: 0.6436 (t80) REVERT: B 388 ASN cc_start: 0.8310 (m-40) cc_final: 0.8078 (t0) REVERT: B 461 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6448 (pp) REVERT: B 752 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9129 (tt) REVERT: B 759 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7412 (t80) REVERT: B 965 GLN cc_start: 0.8638 (tm-30) cc_final: 0.8259 (tm-30) REVERT: C 153 MET cc_start: 0.2600 (mmt) cc_final: 0.2145 (mpp) REVERT: C 177 MET cc_start: 0.7645 (ppp) cc_final: 0.7109 (mpp) REVERT: C 515 PHE cc_start: 0.7934 (m-80) cc_final: 0.7596 (m-10) REVERT: C 574 ASP cc_start: 0.8294 (t0) cc_final: 0.7816 (t0) REVERT: C 752 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9201 (tt) REVERT: C 759 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7536 (t80) REVERT: C 1130 ILE cc_start: 0.8261 (mp) cc_final: 0.7845 (tp) outliers start: 65 outliers final: 50 residues processed: 245 average time/residue: 0.3217 time to fit residues: 134.2326 Evaluate side-chains 244 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 187 time to evaluate : 3.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 325 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 149 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 chunk 325 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 263 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN C 658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.178288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3600 r_free = 0.3600 target = 0.119958 restraints weight = 40257.994| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.09 r_work: 0.3357 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27327 Z= 0.129 Angle : 0.609 11.780 37347 Z= 0.296 Chirality : 0.046 0.320 4365 Planarity : 0.004 0.054 4722 Dihedral : 6.104 69.750 4914 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.42 % Allowed : 14.74 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.15), residues: 3267 helix: 2.14 (0.22), residues: 651 sheet: -0.52 (0.19), residues: 708 loop : -1.36 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 64 HIS 0.003 0.001 HIS A1088 PHE 0.018 0.001 PHE A1121 TYR 0.022 0.001 TYR A 508 ARG 0.004 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 48) link_NAG-ASN : angle 2.83431 ( 144) link_BETA1-4 : bond 0.00345 ( 18) link_BETA1-4 : angle 1.68145 ( 54) hydrogen bonds : bond 0.04382 ( 833) hydrogen bonds : angle 4.53716 ( 2298) SS BOND : bond 0.00203 ( 36) SS BOND : angle 0.85439 ( 72) covalent geometry : bond 0.00301 (27225) covalent geometry : angle 0.58050 (37077) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 189 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2049 (mmt) cc_final: 0.0959 (mpp) REVERT: A 177 MET cc_start: 0.7625 (ppp) cc_final: 0.7302 (ppp) REVERT: A 461 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6534 (pp) REVERT: B 153 MET cc_start: 0.2093 (mmt) cc_final: 0.1476 (mpp) REVERT: B 200 TYR cc_start: 0.6859 (OUTLIER) cc_final: 0.6369 (t80) REVERT: B 388 ASN cc_start: 0.8277 (m-40) cc_final: 0.8035 (t0) REVERT: B 461 LEU cc_start: 0.6866 (OUTLIER) cc_final: 0.6518 (pp) REVERT: B 752 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.9133 (tt) REVERT: B 759 PHE cc_start: 0.7919 (OUTLIER) cc_final: 0.7451 (t80) REVERT: B 965 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8169 (tm-30) REVERT: C 153 MET cc_start: 0.2682 (mmt) cc_final: 0.2282 (mpp) REVERT: C 177 MET cc_start: 0.7621 (ppp) cc_final: 0.7088 (mpp) REVERT: C 515 PHE cc_start: 0.7921 (m-80) cc_final: 0.7558 (m-10) REVERT: C 574 ASP cc_start: 0.8163 (t0) cc_final: 0.7695 (t0) REVERT: C 752 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9167 (tt) REVERT: C 759 PHE cc_start: 0.7878 (OUTLIER) cc_final: 0.7512 (t80) REVERT: C 973 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8984 (mt) REVERT: C 1130 ILE cc_start: 0.8233 (mp) cc_final: 0.7847 (tp) outliers start: 69 outliers final: 59 residues processed: 244 average time/residue: 0.3303 time to fit residues: 136.9892 Evaluate side-chains 253 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 2.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 157 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1118 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 30 ASN Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 263 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 24 optimal weight: 0.0470 chunk 292 optimal weight: 1.9990 chunk 295 optimal weight: 0.0470 chunk 297 optimal weight: 0.1980 chunk 198 optimal weight: 0.6980 chunk 285 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 957 GLN C 658 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.179677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122199 restraints weight = 40236.135| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.13 r_work: 0.3391 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27327 Z= 0.107 Angle : 0.589 11.535 37347 Z= 0.286 Chirality : 0.045 0.317 4365 Planarity : 0.004 0.054 4722 Dihedral : 5.813 59.942 4914 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.35 % Allowed : 14.99 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.15), residues: 3267 helix: 2.20 (0.22), residues: 654 sheet: -0.54 (0.19), residues: 726 loop : -1.29 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP C 64 HIS 0.007 0.001 HIS B 954 PHE 0.016 0.001 PHE C 371 TYR 0.018 0.001 TYR B1067 ARG 0.004 0.000 ARG A 983 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 48) link_NAG-ASN : angle 2.78465 ( 144) link_BETA1-4 : bond 0.00389 ( 18) link_BETA1-4 : angle 1.52910 ( 54) hydrogen bonds : bond 0.03939 ( 833) hydrogen bonds : angle 4.40407 ( 2298) SS BOND : bond 0.00153 ( 36) SS BOND : angle 0.74815 ( 72) covalent geometry : bond 0.00237 (27225) covalent geometry : angle 0.56154 (37077) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 186 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1958 (mmt) cc_final: 0.0935 (mpp) REVERT: A 177 MET cc_start: 0.7628 (ppp) cc_final: 0.7305 (ppp) REVERT: A 461 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6621 (pp) REVERT: B 153 MET cc_start: 0.1976 (mmt) cc_final: 0.1423 (mpp) REVERT: B 200 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.6288 (t80) REVERT: B 388 ASN cc_start: 0.8238 (m-40) cc_final: 0.7988 (t0) REVERT: B 461 LEU cc_start: 0.6845 (OUTLIER) cc_final: 0.6512 (pp) REVERT: B 515 PHE cc_start: 0.7914 (m-80) cc_final: 0.7339 (m-10) REVERT: B 752 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9121 (tt) REVERT: B 759 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7471 (t80) REVERT: C 153 MET cc_start: 0.2686 (mmt) cc_final: 0.2137 (mpp) REVERT: C 177 MET cc_start: 0.7709 (ppp) cc_final: 0.7189 (mpp) REVERT: C 242 LEU cc_start: 0.7980 (tp) cc_final: 0.7623 (mp) REVERT: C 515 PHE cc_start: 0.7895 (m-80) cc_final: 0.7485 (m-10) REVERT: C 574 ASP cc_start: 0.8127 (t0) cc_final: 0.7642 (t0) REVERT: C 752 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9205 (tt) REVERT: C 759 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7627 (t80) REVERT: C 973 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9041 (mt) REVERT: C 1130 ILE cc_start: 0.8178 (mp) cc_final: 0.7797 (tp) outliers start: 67 outliers final: 47 residues processed: 240 average time/residue: 0.3171 time to fit residues: 129.3460 Evaluate side-chains 236 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 PHE Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain C residue 1129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 237 optimal weight: 6.9990 chunk 309 optimal weight: 5.9990 chunk 94 optimal weight: 0.6980 chunk 253 optimal weight: 5.9990 chunk 323 optimal weight: 0.8980 chunk 262 optimal weight: 8.9990 chunk 258 optimal weight: 20.0000 chunk 259 optimal weight: 9.9990 chunk 197 optimal weight: 0.4980 chunk 179 optimal weight: 0.0670 chunk 2 optimal weight: 0.6980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 658 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.180050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.130962 restraints weight = 40490.915| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.72 r_work: 0.3472 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27327 Z= 0.106 Angle : 0.584 10.524 37347 Z= 0.285 Chirality : 0.045 0.319 4365 Planarity : 0.004 0.054 4722 Dihedral : 5.599 59.280 4914 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.17 % Allowed : 15.27 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 3267 helix: 2.28 (0.22), residues: 654 sheet: -0.48 (0.19), residues: 723 loop : -1.26 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP A 64 HIS 0.002 0.000 HIS B 66 PHE 0.016 0.001 PHE A1121 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG A 765 Details of bonding type rmsd link_NAG-ASN : bond 0.00459 ( 48) link_NAG-ASN : angle 2.70680 ( 144) link_BETA1-4 : bond 0.00403 ( 18) link_BETA1-4 : angle 1.40378 ( 54) hydrogen bonds : bond 0.03768 ( 833) hydrogen bonds : angle 4.32143 ( 2298) SS BOND : bond 0.00155 ( 36) SS BOND : angle 0.72508 ( 72) covalent geometry : bond 0.00235 (27225) covalent geometry : angle 0.55808 (37077) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15971.82 seconds wall clock time: 280 minutes 26.93 seconds (16826.93 seconds total)