Starting phenix.real_space_refine on Mon Jun 23 15:07:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wg7_32479/06_2025/7wg7_32479.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wg7_32479/06_2025/7wg7_32479.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wg7_32479/06_2025/7wg7_32479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wg7_32479/06_2025/7wg7_32479.map" model { file = "/net/cci-nas-00/data/ceres_data/7wg7_32479/06_2025/7wg7_32479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wg7_32479/06_2025/7wg7_32479.cif" } resolution = 4.0 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= 0.002 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 118 5.16 5 C 17235 2.51 5 N 4408 2.21 5 O 5280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 27041 Number of models: 1 Model: "" Number of chains: 25 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 58, 'TRANS': 1039} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 58, 'TRANS': 1038} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "C" Number of atoms: 8770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8770 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PTRANS': 58, 'TRANS': 1057} Chain breaks: 4 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 16.08, per 1000 atoms: 0.59 Number of scatterers: 27041 At special positions: 0 Unit cell: (146.59, 147.66, 216.14, 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 118 16.00 O 5280 8.00 N 4408 7.00 C 17235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 163 " 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 163 " 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 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=3, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " 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 U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " NAG-ASN " NAG A1301 " - " ASN A 145 " " NAG A1302 " - " ASN A 17 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG B1301 " - " ASN B 125 " " NAG B1303 " - " ASN B 17 " " NAG B1304 " - " ASN B 343 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 145 " " NAG C1303 " - " ASN C 17 " " NAG C1305 " - " ASN C 61 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 717 " " NAG C1311 " - " ASN C 709 " " NAG D 1 " - " ASN B 233 " " NAG E 1 " - " ASN B 331 " " NAG F 1 " - " ASN B 717 " " NAG H 1 " - " ASN B 801 " " NAG I 1 " - " ASN B1098 " " NAG J 1 " - " ASN B1134 " " NAG K 1 " - " ASN A 233 " " NAG L 1 " - " ASN A 331 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 801 " " NAG Q 1 " - " ASN C 233 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C 801 " " NAG V 1 " - " ASN C1134 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.70 Conformation dependent library (CDL) restraints added in 3.1 seconds 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6230 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 40 sheets defined 23.6% alpha, 19.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 342 removed outlier: 3.767A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.141A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 411 removed outlier: 4.129A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 411 " --> pdb=" O ARG B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.695A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 618 No H-bonds generated for 'chain 'B' and resid 616 through 618' Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.509A pdb=" N ALA B 623 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 4.030A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.586A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.709A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.708A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 removed outlier: 3.602A pdb=" N GLY B 910 " --> pdb=" O PHE B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.822A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.673A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 966 removed outlier: 4.598A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.147A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N PHE B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1029 removed outlier: 3.573A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 990 " --> pdb=" O LYS B 986 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.506A pdb=" N LEU B1145 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 1149 through 1157 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.948A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.807A pdb=" N ALA A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 removed outlier: 4.540A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.556A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.723A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.509A pdb=" N GLN A 901 " --> pdb=" O PRO A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.938A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 938 removed outlier: 3.751A pdb=" N ASN A 925 " --> pdb=" O LYS A 921 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA A 930 " --> pdb=" O GLN A 926 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 932 " --> pdb=" O ASN A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 4.398A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.544A pdb=" N PHE A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.024A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1120 Processing helix chain 'A' and resid 1149 through 1161 removed outlier: 4.232A pdb=" N HIS A1159 " --> pdb=" O TYR A1155 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 364 through 369 removed outlier: 3.669A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 369' Processing helix chain 'C' and resid 616 through 623 Proline residue: C 621 - end of helix Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.525A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.687A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.703A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 849 through 854 removed outlier: 4.127A pdb=" N GLN C 853 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.631A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.807A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 918 removed outlier: 3.814A pdb=" N VAL C 915 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.750A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 966 removed outlier: 4.869A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.859A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 988 through 1033 removed outlier: 4.463A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.313A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1145' Processing helix chain 'C' and resid 1145 through 1161 removed outlier: 4.223A pdb=" N GLU C1151 " --> pdb=" O SER C1147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.581A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN B 185 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 186 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER B 202 " --> pdb=" O PRO B 224 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.653A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 318 removed outlier: 4.517A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 610 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.965A pdb=" N ARG B 328 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.697A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.884A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 711 through 715 Processing sheet with id=AB1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.026A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AB3, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 5.542A pdb=" N GLY B1124 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N PHE B1089 " --> pdb=" O VAL B1122 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B1122 " --> pdb=" O PHE B1089 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB5, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.734A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 186 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER A 202 " --> pdb=" O PRO A 224 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.664A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.841A pdb=" N GLY A 103 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 117 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLU A 132 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N CYS A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 311 through 318 removed outlier: 4.424A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.540A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.800A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.185A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC4, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.189A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AC6, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AC7, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.617A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1087 through 1088 Processing sheet with id=AC9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD1, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.199A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 200 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N VAL C 226 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N SER C 202 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.944A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.239A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE C 106 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 134 through 135 Processing sheet with id=AD5, first strand: chain 'C' and resid 311 through 315 removed outlier: 3.544A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AD7, first strand: chain 'C' and resid 354 through 356 removed outlier: 4.338A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AD9, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.502A pdb=" N GLU C 654 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE2, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.941A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE4, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.531A pdb=" N GLN C1113 " --> pdb=" O VAL C1104 " (cutoff:3.500A) 905 hydrogen bonds defined for protein. 2493 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: 12.57 Time building geometry restraints manager: 8.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8490 1.35 - 1.47: 7101 1.47 - 1.59: 11919 1.59 - 1.72: 0 1.72 - 1.84: 148 Bond restraints: 27658 Sorted by residual: bond pdb=" C LEU A 215 " pdb=" N PRO A 216 " ideal model delta sigma weight residual 1.332 1.400 -0.068 1.12e-02 7.97e+03 3.64e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.513 -0.107 2.00e-02 2.50e+03 2.88e+01 bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.510 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C1 NAG S 2 " pdb=" O5 NAG S 2 " ideal model delta sigma weight residual 1.406 1.509 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.504 -0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 27653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 36921 2.77 - 5.53: 581 5.53 - 8.30: 87 8.30 - 11.07: 17 11.07 - 13.83: 6 Bond angle restraints: 37612 Sorted by residual: angle pdb=" N PRO A 942 " pdb=" CA PRO A 942 " pdb=" CB PRO A 942 " ideal model delta sigma weight residual 101.83 110.19 -8.36 8.40e-01 1.42e+00 9.92e+01 angle pdb=" N PRO C 942 " pdb=" CA PRO C 942 " pdb=" CB PRO C 942 " ideal model delta sigma weight residual 101.83 110.16 -8.33 8.40e-01 1.42e+00 9.84e+01 angle pdb=" N PRO B 892 " pdb=" CA PRO B 892 " pdb=" CB PRO B 892 " ideal model delta sigma weight residual 103.36 110.26 -6.90 8.80e-01 1.29e+00 6.15e+01 angle pdb=" N PRO A 892 " pdb=" CA PRO A 892 " pdb=" CB PRO A 892 " ideal model delta sigma weight residual 103.33 110.53 -7.20 9.30e-01 1.16e+00 6.00e+01 angle pdb=" N VAL A 156 " pdb=" CA VAL A 156 " pdb=" C VAL A 156 " ideal model delta sigma weight residual 111.77 103.78 7.99 1.04e+00 9.25e-01 5.91e+01 ... (remaining 37607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.11: 16138 25.11 - 50.22: 990 50.22 - 75.33: 156 75.33 - 100.43: 83 100.43 - 125.54: 77 Dihedral angle restraints: 17444 sinusoidal: 7771 harmonic: 9673 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -179.50 -87.50 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 9.22 83.78 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CA THR B1117 " pdb=" C THR B1117 " pdb=" N ASP B1118 " pdb=" CA ASP B1118 " ideal model delta harmonic sigma weight residual -180.00 -133.97 -46.03 0 5.00e+00 4.00e-02 8.48e+01 ... (remaining 17441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4228 0.116 - 0.232: 189 0.232 - 0.347: 25 0.347 - 0.463: 2 0.463 - 0.579: 3 Chirality restraints: 4447 Sorted by residual: chirality pdb=" C1 NAG L 1 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG L 1 " pdb=" O5 NAG L 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.38e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" C1 NAG C1308 " pdb=" ND2 ASN C 616 " pdb=" C2 NAG C1308 " pdb=" O5 NAG C1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.55e+00 ... (remaining 4444 not shown) Planarity restraints: 4797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A1142 " 0.062 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO A1143 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO A1143 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A1143 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 997 " 0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C ILE B 997 " -0.058 2.00e-02 2.50e+03 pdb=" O ILE B 997 " 0.022 2.00e-02 2.50e+03 pdb=" N THR B 998 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 998 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C THR B 998 " 0.048 2.00e-02 2.50e+03 pdb=" O THR B 998 " -0.018 2.00e-02 2.50e+03 pdb=" N GLY B 999 " -0.016 2.00e-02 2.50e+03 ... (remaining 4794 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4799 2.77 - 3.30: 25154 3.30 - 3.83: 43886 3.83 - 4.37: 47418 4.37 - 4.90: 81899 Nonbonded interactions: 203156 Sorted by model distance: nonbonded pdb=" OD1 ASN A 354 " pdb=" OG SER A 399 " model vdw 2.237 3.040 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.245 3.040 nonbonded pdb=" O THR A1116 " pdb=" OG1 THR A1120 " model vdw 2.261 3.040 nonbonded pdb=" O GLY C 880 " pdb=" OG SER C 884 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR C 37 " pdb=" O LEU C 54 " model vdw 2.268 3.040 ... (remaining 203151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 702 or resid 704 through 1162 or resid 1301 thr \ ough 1309)) selection = (chain 'B' and (resid 14 through 702 or resid 704 through 1162 or resid 1301 thr \ ough 1309)) selection = (chain 'C' and (resid 14 through 828 or resid 849 through 1162 or resid 1301 thr \ ough 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'O' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.020 Extract box with map and model: 1.160 Check model and map are aligned: 0.200 Set scattering table: 0.280 Process input model: 62.380 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.210 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 27765 Z= 0.247 Angle : 0.922 21.958 37885 Z= 0.467 Chirality : 0.059 0.579 4447 Planarity : 0.006 0.094 4756 Dihedral : 19.046 125.542 11097 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.80 % Favored : 92.17 % Rotamer: Outliers : 0.07 % Allowed : 0.52 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.10 (0.14), residues: 3283 helix: -0.18 (0.19), residues: 671 sheet: -0.17 (0.21), residues: 578 loop : -2.34 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 633 HIS 0.017 0.001 HIS B 625 PHE 0.027 0.001 PHE B 106 TYR 0.018 0.001 TYR C1067 ARG 0.011 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00970 ( 41) link_NAG-ASN : angle 4.41015 ( 123) link_BETA1-4 : bond 0.01064 ( 24) link_BETA1-4 : angle 2.83197 ( 72) hydrogen bonds : bond 0.14200 ( 905) hydrogen bonds : angle 6.83706 ( 2493) SS BOND : bond 0.00412 ( 39) SS BOND : angle 1.53064 ( 78) covalent geometry : bond 0.00486 (27658) covalent geometry : angle 0.87896 (37612) Misc. bond : bond 0.00055 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 2.902 Fit side-chains revert: symmetry clash REVERT: B 87 ASN cc_start: 0.4302 (OUTLIER) cc_final: 0.3625 (p0) REVERT: B 636 TYR cc_start: 0.5742 (t80) cc_final: 0.5472 (m-80) REVERT: A 167 TYR cc_start: 0.8242 (t80) cc_final: 0.7982 (t80) REVERT: C 613 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8049 (pp30) REVERT: C 896 ILE cc_start: 0.8178 (mm) cc_final: 0.7927 (tp) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.3402 time to fit residues: 86.1740 Evaluate side-chains 100 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain C residue 613 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 277 optimal weight: 0.3980 chunk 249 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN B 926 GLN B1108 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 HIS A 536 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 628 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.107305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.082266 restraints weight = 118678.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.081469 restraints weight = 76657.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.081852 restraints weight = 65284.836| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 27765 Z= 0.217 Angle : 0.777 18.181 37885 Z= 0.372 Chirality : 0.050 0.449 4447 Planarity : 0.005 0.085 4756 Dihedral : 16.514 113.809 5086 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.65 % Allowed : 8.95 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.79 (0.14), residues: 3283 helix: 0.52 (0.20), residues: 676 sheet: -0.22 (0.21), residues: 594 loop : -2.24 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 633 HIS 0.005 0.001 HIS C1064 PHE 0.022 0.002 PHE C 165 TYR 0.024 0.002 TYR C1067 ARG 0.005 0.000 ARG C 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00789 ( 41) link_NAG-ASN : angle 3.76837 ( 123) link_BETA1-4 : bond 0.00607 ( 24) link_BETA1-4 : angle 2.96576 ( 72) hydrogen bonds : bond 0.05177 ( 905) hydrogen bonds : angle 5.74663 ( 2493) SS BOND : bond 0.00321 ( 39) SS BOND : angle 1.20873 ( 78) covalent geometry : bond 0.00481 (27658) covalent geometry : angle 0.73559 (37612) Misc. bond : bond 0.00028 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 3.061 Fit side-chains revert: symmetry clash REVERT: A 731 MET cc_start: 0.8723 (ppp) cc_final: 0.8194 (ppp) REVERT: C 613 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7966 (pp30) REVERT: C 867 ASP cc_start: 0.7630 (p0) cc_final: 0.7358 (p0) REVERT: C 979 ASP cc_start: 0.7736 (t0) cc_final: 0.7429 (t0) outliers start: 19 outliers final: 13 residues processed: 112 average time/residue: 0.3488 time to fit residues: 68.2740 Evaluate side-chains 107 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 2.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 206 optimal weight: 4.9990 chunk 268 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 222 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 195 optimal weight: 4.9990 chunk 283 optimal weight: 0.9980 chunk 328 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 HIS B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN C 935 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.105461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.080298 restraints weight = 118324.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.079355 restraints weight = 75977.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.079674 restraints weight = 68948.939| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27765 Z= 0.233 Angle : 0.800 18.170 37885 Z= 0.382 Chirality : 0.051 0.426 4447 Planarity : 0.005 0.083 4756 Dihedral : 14.209 113.518 5084 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 1.79 % Allowed : 14.53 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.81 (0.14), residues: 3283 helix: 0.68 (0.20), residues: 663 sheet: -0.51 (0.21), residues: 596 loop : -2.21 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 633 HIS 0.006 0.001 HIS B1058 PHE 0.027 0.002 PHE A 759 TYR 0.027 0.002 TYR C1067 ARG 0.007 0.001 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00834 ( 41) link_NAG-ASN : angle 4.01542 ( 123) link_BETA1-4 : bond 0.00733 ( 24) link_BETA1-4 : angle 3.18355 ( 72) hydrogen bonds : bond 0.05163 ( 905) hydrogen bonds : angle 5.73425 ( 2493) SS BOND : bond 0.00365 ( 39) SS BOND : angle 1.18176 ( 78) covalent geometry : bond 0.00518 (27658) covalent geometry : angle 0.75523 (37612) Misc. bond : bond 0.00051 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 101 time to evaluate : 2.751 Fit side-chains revert: symmetry clash REVERT: B 1038 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8622 (tptt) REVERT: A 511 VAL cc_start: 0.8473 (OUTLIER) cc_final: 0.8241 (t) REVERT: A 731 MET cc_start: 0.8817 (ppp) cc_final: 0.8247 (ppp) REVERT: C 128 ILE cc_start: 0.8973 (mm) cc_final: 0.8697 (tp) REVERT: C 583 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7407 (pm20) REVERT: C 613 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8127 (pp30) REVERT: C 867 ASP cc_start: 0.7905 (p0) cc_final: 0.7576 (p0) REVERT: C 994 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8198 (t70) outliers start: 52 outliers final: 30 residues processed: 144 average time/residue: 0.3151 time to fit residues: 79.8476 Evaluate side-chains 130 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 96 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 62 optimal weight: 3.9990 chunk 256 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 190 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 133 optimal weight: 3.9990 chunk 253 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 238 GLN B 955 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.106883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.081986 restraints weight = 118862.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.081816 restraints weight = 78812.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.082181 restraints weight = 70404.325| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27765 Z= 0.144 Angle : 0.707 18.682 37885 Z= 0.334 Chirality : 0.048 0.409 4447 Planarity : 0.004 0.081 4756 Dihedral : 12.735 111.124 5084 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 1.48 % Allowed : 17.08 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.59 (0.15), residues: 3283 helix: 1.01 (0.21), residues: 666 sheet: -0.27 (0.21), residues: 581 loop : -2.16 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 64 HIS 0.004 0.001 HIS A 143 PHE 0.022 0.001 PHE A 759 TYR 0.015 0.001 TYR C1067 ARG 0.007 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 41) link_NAG-ASN : angle 3.74870 ( 123) link_BETA1-4 : bond 0.00715 ( 24) link_BETA1-4 : angle 3.08019 ( 72) hydrogen bonds : bond 0.04486 ( 905) hydrogen bonds : angle 5.42929 ( 2493) SS BOND : bond 0.00272 ( 39) SS BOND : angle 1.35700 ( 78) covalent geometry : bond 0.00316 (27658) covalent geometry : angle 0.65977 (37612) Misc. bond : bond 0.00033 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 2.784 Fit side-chains revert: symmetry clash REVERT: B 1029 MET cc_start: 0.8916 (tpp) cc_final: 0.8658 (tpt) REVERT: B 1038 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8608 (tptt) REVERT: A 495 TYR cc_start: 0.6611 (OUTLIER) cc_final: 0.4764 (m-80) REVERT: A 731 MET cc_start: 0.8786 (ppp) cc_final: 0.8233 (ppp) REVERT: C 613 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.7924 (pp30) REVERT: C 867 ASP cc_start: 0.7865 (p0) cc_final: 0.7506 (p0) REVERT: C 994 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.8002 (t70) REVERT: C 1031 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7366 (mt-10) REVERT: C 1145 LEU cc_start: 0.4315 (OUTLIER) cc_final: 0.3669 (tp) outliers start: 43 outliers final: 18 residues processed: 137 average time/residue: 0.3103 time to fit residues: 75.4792 Evaluate side-chains 115 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 42 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 270 optimal weight: 0.8980 chunk 323 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 264 optimal weight: 0.2980 chunk 198 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 276 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.108309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.083722 restraints weight = 117837.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.082100 restraints weight = 82837.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.082766 restraints weight = 68033.584| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 27765 Z= 0.113 Angle : 0.680 19.004 37885 Z= 0.319 Chirality : 0.048 0.407 4447 Planarity : 0.004 0.080 4756 Dihedral : 11.766 109.557 5084 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.48 % Allowed : 17.73 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.41 (0.15), residues: 3283 helix: 1.19 (0.21), residues: 663 sheet: -0.07 (0.21), residues: 599 loop : -2.08 (0.13), residues: 2021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 64 HIS 0.002 0.001 HIS B 204 PHE 0.018 0.001 PHE B 374 TYR 0.021 0.001 TYR A 167 ARG 0.006 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00719 ( 41) link_NAG-ASN : angle 3.71996 ( 123) link_BETA1-4 : bond 0.00749 ( 24) link_BETA1-4 : angle 2.91526 ( 72) hydrogen bonds : bond 0.04065 ( 905) hydrogen bonds : angle 5.20310 ( 2493) SS BOND : bond 0.00245 ( 39) SS BOND : angle 1.24738 ( 78) covalent geometry : bond 0.00243 (27658) covalent geometry : angle 0.63337 (37612) Misc. bond : bond 0.00029 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 107 time to evaluate : 2.689 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1029 MET cc_start: 0.8763 (tpp) cc_final: 0.8505 (tpt) REVERT: B 1038 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8586 (tptt) REVERT: A 167 TYR cc_start: 0.8056 (t80) cc_final: 0.7804 (t80) REVERT: A 511 VAL cc_start: 0.8427 (OUTLIER) cc_final: 0.8201 (t) REVERT: A 731 MET cc_start: 0.8866 (ppp) cc_final: 0.8220 (ppp) REVERT: C 583 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7273 (pm20) REVERT: C 613 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7965 (pp30) REVERT: C 731 MET cc_start: 0.8655 (ppp) cc_final: 0.8365 (ppp) REVERT: C 867 ASP cc_start: 0.7788 (p0) cc_final: 0.7436 (p0) REVERT: C 994 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7932 (t70) REVERT: C 1031 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7016 (mt-10) outliers start: 43 outliers final: 20 residues processed: 140 average time/residue: 0.3169 time to fit residues: 77.9555 Evaluate side-chains 121 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1120 THR Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 99 optimal weight: 0.9980 chunk 37 optimal weight: 0.0570 chunk 17 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 246 optimal weight: 0.8980 chunk 206 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 306 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.107105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.082552 restraints weight = 118536.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.081972 restraints weight = 74140.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.082331 restraints weight = 65922.530| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27765 Z= 0.146 Angle : 0.691 18.796 37885 Z= 0.326 Chirality : 0.047 0.399 4447 Planarity : 0.004 0.079 4756 Dihedral : 11.401 109.935 5084 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 2.10 % Allowed : 17.84 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.49 (0.15), residues: 3283 helix: 1.04 (0.21), residues: 673 sheet: -0.18 (0.21), residues: 590 loop : -2.09 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.003 0.001 HIS B1058 PHE 0.027 0.001 PHE A 759 TYR 0.017 0.001 TYR C1067 ARG 0.004 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 41) link_NAG-ASN : angle 3.77430 ( 123) link_BETA1-4 : bond 0.00661 ( 24) link_BETA1-4 : angle 2.98125 ( 72) hydrogen bonds : bond 0.04201 ( 905) hydrogen bonds : angle 5.25911 ( 2493) SS BOND : bond 0.00251 ( 39) SS BOND : angle 1.21639 ( 78) covalent geometry : bond 0.00325 (27658) covalent geometry : angle 0.64354 (37612) Misc. bond : bond 0.00062 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 101 time to evaluate : 4.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1029 MET cc_start: 0.8904 (tpp) cc_final: 0.8578 (tpp) REVERT: B 1038 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8627 (tptt) REVERT: A 461 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6104 (tp) REVERT: A 495 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.4584 (m-10) REVERT: A 511 VAL cc_start: 0.8454 (OUTLIER) cc_final: 0.8245 (t) REVERT: A 731 MET cc_start: 0.8847 (ppp) cc_final: 0.8213 (ppp) REVERT: C 115 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.5711 (mp10) REVERT: C 128 ILE cc_start: 0.8900 (mm) cc_final: 0.8600 (tp) REVERT: C 583 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7273 (pm20) REVERT: C 613 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8069 (pp30) REVERT: C 731 MET cc_start: 0.8733 (ppp) cc_final: 0.8371 (ppp) REVERT: C 867 ASP cc_start: 0.7981 (p0) cc_final: 0.7621 (p0) REVERT: C 994 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8104 (t70) REVERT: C 1031 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7188 (mt-10) REVERT: C 1145 LEU cc_start: 0.4384 (OUTLIER) cc_final: 0.3712 (tp) outliers start: 61 outliers final: 37 residues processed: 154 average time/residue: 0.4620 time to fit residues: 125.2723 Evaluate side-chains 141 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 96 time to evaluate : 3.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain C residue 115 GLN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 168 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 206 optimal weight: 0.0770 chunk 307 optimal weight: 0.3980 chunk 54 optimal weight: 3.9990 chunk 319 optimal weight: 4.9990 chunk 277 optimal weight: 1.9990 chunk 188 optimal weight: 3.9990 chunk 285 optimal weight: 0.8980 overall best weight: 1.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.107470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.082984 restraints weight = 118389.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.081153 restraints weight = 81889.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.081661 restraints weight = 71566.058| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27765 Z= 0.130 Angle : 0.680 19.544 37885 Z= 0.321 Chirality : 0.047 0.403 4447 Planarity : 0.004 0.078 4756 Dihedral : 10.966 110.108 5084 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.55 % Allowed : 17.91 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.43 (0.15), residues: 3283 helix: 1.14 (0.21), residues: 669 sheet: -0.11 (0.21), residues: 587 loop : -2.07 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.003 0.001 HIS C1083 PHE 0.023 0.001 PHE A 759 TYR 0.015 0.001 TYR C1067 ARG 0.004 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00702 ( 41) link_NAG-ASN : angle 3.74420 ( 123) link_BETA1-4 : bond 0.00700 ( 24) link_BETA1-4 : angle 2.94331 ( 72) hydrogen bonds : bond 0.04065 ( 905) hydrogen bonds : angle 5.17962 ( 2493) SS BOND : bond 0.00275 ( 39) SS BOND : angle 1.20316 ( 78) covalent geometry : bond 0.00288 (27658) covalent geometry : angle 0.63293 (37612) Misc. bond : bond 0.00018 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 103 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8425 (mm) REVERT: B 774 GLN cc_start: 0.8659 (mm-40) cc_final: 0.8421 (tp-100) REVERT: B 1038 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8592 (tptt) REVERT: A 167 TYR cc_start: 0.8082 (t80) cc_final: 0.7826 (t80) REVERT: A 461 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6064 (tp) REVERT: A 495 TYR cc_start: 0.6542 (OUTLIER) cc_final: 0.4562 (m-10) REVERT: A 511 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8309 (t) REVERT: A 731 MET cc_start: 0.8826 (ppp) cc_final: 0.8222 (ppp) REVERT: C 128 ILE cc_start: 0.8878 (mm) cc_final: 0.8498 (tp) REVERT: C 547 LYS cc_start: 0.8765 (ptpp) cc_final: 0.8507 (mtmt) REVERT: C 583 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7291 (pm20) REVERT: C 613 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7998 (pp30) REVERT: C 731 MET cc_start: 0.8697 (ppp) cc_final: 0.8365 (ppp) REVERT: C 867 ASP cc_start: 0.7848 (p0) cc_final: 0.7492 (p0) REVERT: C 1031 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7020 (mt-10) REVERT: C 1145 LEU cc_start: 0.4227 (OUTLIER) cc_final: 0.3653 (tp) outliers start: 74 outliers final: 43 residues processed: 166 average time/residue: 0.3326 time to fit residues: 96.9982 Evaluate side-chains 148 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 98 time to evaluate : 2.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1012 LEU Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 157 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 278 optimal weight: 0.8980 chunk 291 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 285 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 313 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 322 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.106261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.080704 restraints weight = 107673.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.079387 restraints weight = 78753.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079847 restraints weight = 66974.496| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27765 Z= 0.114 Angle : 0.669 19.821 37885 Z= 0.314 Chirality : 0.047 0.426 4447 Planarity : 0.004 0.078 4756 Dihedral : 10.505 109.074 5084 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 2.00 % Allowed : 18.56 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.35 (0.15), residues: 3283 helix: 1.27 (0.21), residues: 664 sheet: -0.01 (0.22), residues: 578 loop : -2.05 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.002 0.000 HIS B1088 PHE 0.018 0.001 PHE A 759 TYR 0.015 0.001 TYR B 636 ARG 0.003 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 41) link_NAG-ASN : angle 3.71503 ( 123) link_BETA1-4 : bond 0.00747 ( 24) link_BETA1-4 : angle 2.91267 ( 72) hydrogen bonds : bond 0.03836 ( 905) hydrogen bonds : angle 5.08917 ( 2493) SS BOND : bond 0.00240 ( 39) SS BOND : angle 1.11460 ( 78) covalent geometry : bond 0.00251 (27658) covalent geometry : angle 0.62196 (37612) Misc. bond : bond 0.00018 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 111 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8490 (mm) REVERT: B 1038 LYS cc_start: 0.8849 (mmmt) cc_final: 0.8540 (tptt) REVERT: A 167 TYR cc_start: 0.8052 (t80) cc_final: 0.7773 (t80) REVERT: A 461 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6065 (tp) REVERT: A 495 TYR cc_start: 0.6332 (OUTLIER) cc_final: 0.4397 (m-10) REVERT: A 731 MET cc_start: 0.8837 (ppp) cc_final: 0.8181 (ppp) REVERT: C 128 ILE cc_start: 0.8939 (mm) cc_final: 0.8576 (tp) REVERT: C 583 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7337 (pm20) REVERT: C 613 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.8027 (pp30) REVERT: C 731 MET cc_start: 0.8767 (ppp) cc_final: 0.8406 (ppp) REVERT: C 867 ASP cc_start: 0.7910 (p0) cc_final: 0.7558 (p0) REVERT: C 1031 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7463 (mt-10) REVERT: C 1145 LEU cc_start: 0.4498 (OUTLIER) cc_final: 0.3715 (tp) outliers start: 58 outliers final: 40 residues processed: 159 average time/residue: 0.3657 time to fit residues: 103.6094 Evaluate side-chains 145 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 99 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 909 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 214 optimal weight: 0.0670 chunk 254 optimal weight: 6.9990 chunk 271 optimal weight: 10.0000 chunk 268 optimal weight: 0.7980 chunk 27 optimal weight: 4.9990 chunk 252 optimal weight: 4.9990 chunk 159 optimal weight: 0.7980 chunk 187 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.9322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.107029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.081969 restraints weight = 119224.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.081203 restraints weight = 76796.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.081501 restraints weight = 67210.106| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27765 Z= 0.154 Angle : 0.703 19.600 37885 Z= 0.333 Chirality : 0.048 0.505 4447 Planarity : 0.004 0.077 4756 Dihedral : 10.333 110.405 5084 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.20 % Allowed : 18.73 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.41 (0.15), residues: 3283 helix: 1.12 (0.21), residues: 677 sheet: -0.12 (0.21), residues: 592 loop : -2.06 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 64 HIS 0.005 0.001 HIS A 625 PHE 0.024 0.001 PHE A 759 TYR 0.019 0.001 TYR C 396 ARG 0.003 0.000 ARG C 403 Details of bonding type rmsd link_NAG-ASN : bond 0.00715 ( 41) link_NAG-ASN : angle 3.80102 ( 123) link_BETA1-4 : bond 0.00662 ( 24) link_BETA1-4 : angle 2.95647 ( 72) hydrogen bonds : bond 0.04134 ( 905) hydrogen bonds : angle 5.20569 ( 2493) SS BOND : bond 0.00272 ( 39) SS BOND : angle 1.09961 ( 78) covalent geometry : bond 0.00347 (27658) covalent geometry : angle 0.65652 (37612) Misc. bond : bond 0.00019 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 99 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6691 (t70) REVERT: B 387 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8361 (mm) REVERT: B 1030 SER cc_start: 0.9291 (m) cc_final: 0.8716 (t) REVERT: B 1038 LYS cc_start: 0.8894 (mmmt) cc_final: 0.8595 (tptt) REVERT: A 167 TYR cc_start: 0.8050 (t80) cc_final: 0.7784 (t80) REVERT: A 495 TYR cc_start: 0.6561 (OUTLIER) cc_final: 0.4544 (m-10) REVERT: A 731 MET cc_start: 0.8838 (ppp) cc_final: 0.8201 (ppp) REVERT: C 128 ILE cc_start: 0.8889 (mm) cc_final: 0.8536 (tp) REVERT: C 583 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: C 613 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8140 (pp30) REVERT: C 867 ASP cc_start: 0.8028 (p0) cc_final: 0.7646 (p0) REVERT: C 1031 GLU cc_start: 0.7700 (mt-10) cc_final: 0.7423 (mt-10) REVERT: C 1041 ASP cc_start: 0.7832 (t0) cc_final: 0.7530 (t0) REVERT: C 1145 LEU cc_start: 0.4377 (OUTLIER) cc_final: 0.3751 (tp) outliers start: 64 outliers final: 47 residues processed: 156 average time/residue: 0.3415 time to fit residues: 95.0025 Evaluate side-chains 149 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 96 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 185 ASN Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 263 optimal weight: 50.0000 chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 217 optimal weight: 30.0000 chunk 256 optimal weight: 0.0000 chunk 117 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 277 optimal weight: 10.0000 chunk 287 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.106851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.081847 restraints weight = 118242.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.081136 restraints weight = 79066.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.081450 restraints weight = 71079.468| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 27765 Z= 0.192 Angle : 0.811 59.198 37885 Z= 0.411 Chirality : 0.048 0.479 4447 Planarity : 0.004 0.077 4756 Dihedral : 10.326 110.284 5084 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 2.03 % Allowed : 18.94 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.44 (0.15), residues: 3283 helix: 1.09 (0.21), residues: 677 sheet: -0.15 (0.21), residues: 593 loop : -2.07 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.003 0.001 HIS B1058 PHE 0.022 0.001 PHE A 759 TYR 0.019 0.001 TYR C 396 ARG 0.003 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 41) link_NAG-ASN : angle 3.80653 ( 123) link_BETA1-4 : bond 0.00640 ( 24) link_BETA1-4 : angle 2.98377 ( 72) hydrogen bonds : bond 0.04165 ( 905) hydrogen bonds : angle 5.20641 ( 2493) SS BOND : bond 0.00285 ( 39) SS BOND : angle 1.11504 ( 78) covalent geometry : bond 0.00430 (27658) covalent geometry : angle 0.77204 (37612) Misc. bond : bond 0.00028 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6566 Ramachandran restraints generated. 3283 Oldfield, 0 Emsley, 3283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 97 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 80 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6615 (t70) REVERT: B 387 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8373 (mm) REVERT: B 1030 SER cc_start: 0.9303 (m) cc_final: 0.8739 (t) REVERT: B 1038 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8611 (tptt) REVERT: A 167 TYR cc_start: 0.8039 (t80) cc_final: 0.7780 (t80) REVERT: A 495 TYR cc_start: 0.6560 (OUTLIER) cc_final: 0.4529 (m-10) REVERT: A 731 MET cc_start: 0.8850 (ppp) cc_final: 0.8206 (ppp) REVERT: C 128 ILE cc_start: 0.8903 (mm) cc_final: 0.8559 (tp) REVERT: C 583 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7258 (pm20) REVERT: C 613 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8151 (pp30) REVERT: C 867 ASP cc_start: 0.8053 (p0) cc_final: 0.7684 (p0) REVERT: C 1031 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7466 (mt-10) REVERT: C 1041 ASP cc_start: 0.7849 (t0) cc_final: 0.7535 (t0) REVERT: C 1145 LEU cc_start: 0.4414 (OUTLIER) cc_final: 0.3765 (tp) outliers start: 59 outliers final: 48 residues processed: 149 average time/residue: 0.3083 time to fit residues: 81.3634 Evaluate side-chains 150 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 96 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 104 TRP Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1055 SER Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 467 ASP Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 508 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 752 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 827 THR Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1066 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 168 optimal weight: 0.0770 chunk 201 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 282 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 277 optimal weight: 5.9990 chunk 251 optimal weight: 7.9990 chunk 222 optimal weight: 7.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.106833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.081764 restraints weight = 118682.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.081027 restraints weight = 76620.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.081359 restraints weight = 66656.984| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 27765 Z= 0.192 Angle : 0.811 59.198 37885 Z= 0.411 Chirality : 0.048 0.479 4447 Planarity : 0.004 0.077 4756 Dihedral : 10.326 110.284 5084 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.32 % Favored : 91.68 % Rotamer: Outliers : 1.93 % Allowed : 19.04 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.44 (0.15), residues: 3283 helix: 1.09 (0.21), residues: 677 sheet: -0.15 (0.21), residues: 593 loop : -2.07 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 64 HIS 0.003 0.001 HIS B1058 PHE 0.022 0.001 PHE A 759 TYR 0.019 0.001 TYR C 396 ARG 0.003 0.000 ARG B 78 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 41) link_NAG-ASN : angle 3.80653 ( 123) link_BETA1-4 : bond 0.00640 ( 24) link_BETA1-4 : angle 2.98377 ( 72) hydrogen bonds : bond 0.04165 ( 905) hydrogen bonds : angle 5.20641 ( 2493) SS BOND : bond 0.00294 ( 39) SS BOND : angle 1.13879 ( 78) covalent geometry : bond 0.00430 (27658) covalent geometry : angle 0.77204 (37612) Misc. bond : bond 0.00028 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7717.82 seconds wall clock time: 137 minutes 44.90 seconds (8264.90 seconds total)