Starting phenix.real_space_refine on Fri Mar 6 02:07:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wg7_32479/03_2026/7wg7_32479.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wg7_32479/03_2026/7wg7_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_32479/03_2026/7wg7_32479.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wg7_32479/03_2026/7wg7_32479.map" model { file = "/net/cci-nas-00/data/ceres_data/7wg7_32479/03_2026/7wg7_32479.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wg7_32479/03_2026/7wg7_32479.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 6.17, per 1000 atoms: 0.23 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: 2.13 Conformation dependent library (CDL) restraints added in 1.2 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: 0.76 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: 5.55 Time building geometry restraints manager: 2.87 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 1309)) selection = (chain 'B' and (resid 14 through 702 or resid 704 through 1309)) selection = (chain 'C' and (resid 14 through 828 or resid 849 through 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: 2.080 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: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 24.260 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- 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 : 6.78 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.011 0.000 ARG C 403 TYR 0.018 0.001 TYR C1067 PHE 0.027 0.001 PHE B 106 TRP 0.013 0.001 TRP C 633 HIS 0.017 0.001 HIS B 625 Details of bonding type rmsd covalent geometry : bond 0.00486 (27658) covalent geometry : angle 0.87896 (37612) SS BOND : bond 0.00412 ( 39) SS BOND : angle 1.53064 ( 78) hydrogen bonds : bond 0.14200 ( 905) hydrogen bonds : angle 6.83706 ( 2493) Misc. bond : bond 0.00055 ( 3) link_BETA1-4 : bond 0.01064 ( 24) link_BETA1-4 : angle 2.83197 ( 72) link_NAG-ASN : bond 0.00970 ( 41) link_NAG-ASN : angle 4.41015 ( 123) *********************** 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 : 1.040 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: 0.1515 time to fit residues: 38.5389 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 : 0.941 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.0070 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 4.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN C 628 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.110433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.085366 restraints weight = 118634.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.084403 restraints weight = 78016.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.085125 restraints weight = 67353.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.084892 restraints weight = 63873.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.085199 restraints weight = 52544.681| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27765 Z= 0.122 Angle : 0.705 18.438 37885 Z= 0.332 Chirality : 0.049 0.433 4447 Planarity : 0.004 0.084 4756 Dihedral : 16.398 110.508 5086 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.41 % Allowed : 6.68 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3283 helix: 0.68 (0.21), residues: 674 sheet: 0.02 (0.21), residues: 593 loop : -2.19 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.017 0.001 TYR C 269 PHE 0.019 0.001 PHE A 219 TRP 0.010 0.001 TRP C 633 HIS 0.004 0.001 HIS B 954 Details of bonding type rmsd covalent geometry : bond 0.00260 (27658) covalent geometry : angle 0.66356 (37612) SS BOND : bond 0.00242 ( 39) SS BOND : angle 1.00694 ( 78) hydrogen bonds : bond 0.04493 ( 905) hydrogen bonds : angle 5.48050 ( 2493) Misc. bond : bond 0.00024 ( 3) link_BETA1-4 : bond 0.00693 ( 24) link_BETA1-4 : angle 2.81987 ( 72) link_NAG-ASN : bond 0.00682 ( 41) link_NAG-ASN : angle 3.61655 ( 123) *********************** 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: 12 poor density : 110 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: B 964 LYS cc_start: 0.9082 (tppt) cc_final: 0.8776 (tppt) REVERT: A 731 MET cc_start: 0.8816 (ppp) cc_final: 0.8231 (ppp) REVERT: C 613 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7858 (pp30) REVERT: C 867 ASP cc_start: 0.7654 (p0) cc_final: 0.7426 (p0) REVERT: C 896 ILE cc_start: 0.8031 (mm) cc_final: 0.7830 (tp) REVERT: C 979 ASP cc_start: 0.7842 (t0) cc_final: 0.7444 (t0) outliers start: 12 outliers final: 9 residues processed: 114 average time/residue: 0.1616 time to fit residues: 31.6516 Evaluate side-chains 108 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 TRP 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 A residue 197 TYR Chi-restraints excluded: chain A residue 390 LEU 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 121 optimal weight: 20.0000 chunk 305 optimal weight: 4.9990 chunk 317 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 316 optimal weight: 0.0030 chunk 49 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 overall best weight: 3.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN B 185 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.106138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.080936 restraints weight = 119324.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.079988 restraints weight = 75830.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.080360 restraints weight = 68197.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.080545 restraints weight = 60960.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.080642 restraints weight = 54681.377| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 27765 Z= 0.250 Angle : 0.793 18.085 37885 Z= 0.380 Chirality : 0.050 0.427 4447 Planarity : 0.005 0.082 4756 Dihedral : 14.510 113.483 5084 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 1.10 % Allowed : 12.50 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.14), residues: 3283 helix: 0.66 (0.20), residues: 667 sheet: -0.33 (0.21), residues: 583 loop : -2.17 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 634 TYR 0.029 0.002 TYR B1138 PHE 0.031 0.002 PHE A 759 TRP 0.013 0.002 TRP C 633 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00559 (27658) covalent geometry : angle 0.75147 (37612) SS BOND : bond 0.00356 ( 39) SS BOND : angle 1.13252 ( 78) hydrogen bonds : bond 0.05135 ( 905) hydrogen bonds : angle 5.67529 ( 2493) Misc. bond : bond 0.00034 ( 3) link_BETA1-4 : bond 0.00580 ( 24) link_BETA1-4 : angle 3.16666 ( 72) link_NAG-ASN : bond 0.00858 ( 41) link_NAG-ASN : angle 3.79372 ( 123) *********************** 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 130 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.966 Fit side-chains REVERT: A 511 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8392 (t) REVERT: A 731 MET cc_start: 0.8736 (ppp) cc_final: 0.8274 (ppp) REVERT: A 882 ILE cc_start: 0.9213 (tp) cc_final: 0.8995 (mt) REVERT: C 128 ILE cc_start: 0.8931 (mm) cc_final: 0.8653 (tp) REVERT: C 583 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7214 (pm20) REVERT: C 613 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8055 (pp30) REVERT: C 867 ASP cc_start: 0.7798 (p0) cc_final: 0.7498 (p0) outliers start: 32 outliers final: 17 residues processed: 121 average time/residue: 0.1532 time to fit residues: 32.6011 Evaluate side-chains 110 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.972 ------------------------------------------------------------------------------- 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 991 VAL Chi-restraints excluded: chain B residue 1120 THR 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 934 ILE Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1137 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 864 LEU Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 132 optimal weight: 5.9990 chunk 315 optimal weight: 3.9990 chunk 197 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 77 optimal weight: 0.0980 chunk 272 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1108 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.107382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.082451 restraints weight = 118518.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.081984 restraints weight = 73945.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.082330 restraints weight = 65707.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.082568 restraints weight = 57994.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.082584 restraints weight = 52775.288| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1661 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= 0.153 Angle : 0.716 18.729 37885 Z= 0.337 Chirality : 0.048 0.412 4447 Planarity : 0.004 0.081 4756 Dihedral : 13.051 110.908 5084 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.27 % Allowed : 14.98 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3283 helix: 0.97 (0.21), residues: 665 sheet: -0.27 (0.21), residues: 589 loop : -2.11 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 403 TYR 0.018 0.001 TYR C1067 PHE 0.021 0.001 PHE A 759 TRP 0.016 0.001 TRP B 64 HIS 0.005 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00339 (27658) covalent geometry : angle 0.66798 (37612) SS BOND : bond 0.00308 ( 39) SS BOND : angle 1.35368 ( 78) hydrogen bonds : bond 0.04447 ( 905) hydrogen bonds : angle 5.41241 ( 2493) Misc. bond : bond 0.00038 ( 3) link_BETA1-4 : bond 0.00663 ( 24) link_BETA1-4 : angle 3.06100 ( 72) link_NAG-ASN : bond 0.00727 ( 41) link_NAG-ASN : angle 3.82476 ( 123) *********************** 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 138 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.953 Fit side-chains REVERT: B 1038 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8545 (tptt) REVERT: A 731 MET cc_start: 0.8755 (ppp) cc_final: 0.8198 (ppp) REVERT: C 128 ILE cc_start: 0.8969 (mm) cc_final: 0.8689 (tp) REVERT: C 613 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7931 (pp30) REVERT: C 731 MET cc_start: 0.8561 (ppp) cc_final: 0.8334 (ppp) REVERT: C 867 ASP cc_start: 0.7820 (p0) cc_final: 0.7494 (p0) REVERT: C 994 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7957 (t70) REVERT: C 1145 LEU cc_start: 0.4291 (OUTLIER) cc_final: 0.3647 (tp) outliers start: 37 outliers final: 19 residues processed: 130 average time/residue: 0.1495 time to fit residues: 34.2964 Evaluate side-chains 116 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 751 ASN 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 866 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain C residue 190 VAL 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 977 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 198 optimal weight: 0.8980 chunk 194 optimal weight: 0.6980 chunk 43 optimal weight: 0.0270 chunk 246 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 210 optimal weight: 6.9990 overall best weight: 1.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A1023 ASN ** 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 895 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.107599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.082670 restraints weight = 118245.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.082443 restraints weight = 75358.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.082750 restraints weight = 62777.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.082915 restraints weight = 57490.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083001 restraints weight = 51802.412| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27765 Z= 0.135 Angle : 0.691 18.752 37885 Z= 0.325 Chirality : 0.047 0.399 4447 Planarity : 0.004 0.079 4756 Dihedral : 12.144 110.475 5084 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.62 % Allowed : 16.08 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.15), residues: 3283 helix: 1.04 (0.21), residues: 666 sheet: -0.23 (0.21), residues: 588 loop : -2.06 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.017 0.001 TYR C1067 PHE 0.020 0.001 PHE A 759 TRP 0.017 0.001 TRP B 64 HIS 0.003 0.001 HIS A 204 Details of bonding type rmsd covalent geometry : bond 0.00299 (27658) covalent geometry : angle 0.64450 (37612) SS BOND : bond 0.00252 ( 39) SS BOND : angle 1.13766 ( 78) hydrogen bonds : bond 0.04274 ( 905) hydrogen bonds : angle 5.30287 ( 2493) Misc. bond : bond 0.00025 ( 3) link_BETA1-4 : bond 0.00684 ( 24) link_BETA1-4 : angle 2.96407 ( 72) link_NAG-ASN : bond 0.00721 ( 41) link_NAG-ASN : angle 3.73065 ( 123) *********************** 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 151 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1029 MET cc_start: 0.8928 (tpp) cc_final: 0.8575 (tpt) REVERT: B 1038 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8584 (tptt) REVERT: A 511 VAL cc_start: 0.8557 (OUTLIER) cc_final: 0.8337 (t) REVERT: C 583 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: C 613 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7960 (pp30) REVERT: C 731 MET cc_start: 0.8594 (ppp) cc_final: 0.8326 (ppp) REVERT: C 867 ASP cc_start: 0.7954 (p0) cc_final: 0.7598 (p0) REVERT: C 994 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8051 (t70) REVERT: C 1031 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7245 (mt-10) outliers start: 47 outliers final: 23 residues processed: 139 average time/residue: 0.1524 time to fit residues: 37.1268 Evaluate side-chains 122 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 731 MET Chi-restraints excluded: chain B residue 1012 LEU 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 219 PHE 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 697 MET Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 266 TYR 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 729 VAL 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 30 optimal weight: 7.9990 chunk 80 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 108 optimal weight: 0.4980 chunk 269 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 218 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 267 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1074 ASN A1023 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.105125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.079972 restraints weight = 118830.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.079178 restraints weight = 76006.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.079591 restraints weight = 67783.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079806 restraints weight = 59804.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079840 restraints weight = 53690.530| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 27765 Z= 0.225 Angle : 0.773 18.194 37885 Z= 0.371 Chirality : 0.049 0.405 4447 Planarity : 0.004 0.079 4756 Dihedral : 11.946 113.234 5084 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 2.20 % Allowed : 17.22 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3283 helix: 0.77 (0.20), residues: 668 sheet: -0.46 (0.21), residues: 588 loop : -2.18 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.022 0.002 TYR C1067 PHE 0.025 0.002 PHE A 759 TRP 0.019 0.002 TRP B 64 HIS 0.006 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00503 (27658) covalent geometry : angle 0.72715 (37612) SS BOND : bond 0.00592 ( 39) SS BOND : angle 1.55905 ( 78) hydrogen bonds : bond 0.04984 ( 905) hydrogen bonds : angle 5.63458 ( 2493) Misc. bond : bond 0.00034 ( 3) link_BETA1-4 : bond 0.00603 ( 24) link_BETA1-4 : angle 3.08050 ( 72) link_NAG-ASN : bond 0.00839 ( 41) link_NAG-ASN : angle 3.92846 ( 123) *********************** 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 161 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 97 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 784 GLN cc_start: 0.7938 (mp10) cc_final: 0.7682 (mp-120) REVERT: B 1029 MET cc_start: 0.8822 (tpp) cc_final: 0.8487 (tpp) REVERT: A 461 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6141 (tp) REVERT: A 495 TYR cc_start: 0.6905 (OUTLIER) cc_final: 0.4829 (m-10) REVERT: A 511 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8196 (t) REVERT: C 583 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: C 613 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8143 (pp30) REVERT: C 867 ASP cc_start: 0.8024 (p0) cc_final: 0.7685 (p0) REVERT: C 976 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8398 (m) REVERT: C 994 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8203 (t70) REVERT: C 1031 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7485 (mt-10) REVERT: C 1145 LEU cc_start: 0.4431 (OUTLIER) cc_final: 0.3698 (tp) outliers start: 64 outliers final: 37 residues processed: 154 average time/residue: 0.1460 time to fit residues: 39.8336 Evaluate side-chains 138 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 93 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 729 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 1012 LEU 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 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 390 LEU 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 724 THR Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 266 TYR 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 729 VAL 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 864 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU 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 19 optimal weight: 20.0000 chunk 213 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 300 optimal weight: 0.7980 chunk 264 optimal weight: 9.9990 chunk 84 optimal weight: 0.2980 chunk 67 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 294 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.107390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.082784 restraints weight = 117793.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.081513 restraints weight = 78885.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.082212 restraints weight = 65517.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.082383 restraints weight = 56150.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.082444 restraints weight = 51531.154| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27765 Z= 0.123 Angle : 0.693 19.840 37885 Z= 0.328 Chirality : 0.048 0.472 4447 Planarity : 0.004 0.079 4756 Dihedral : 11.381 110.678 5084 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.79 % Allowed : 17.91 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.15), residues: 3283 helix: 1.11 (0.21), residues: 671 sheet: -0.20 (0.22), residues: 555 loop : -2.07 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.017 0.001 TYR C 396 PHE 0.030 0.001 PHE A 219 TRP 0.021 0.001 TRP B 64 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00266 (27658) covalent geometry : angle 0.64581 (37612) SS BOND : bond 0.00293 ( 39) SS BOND : angle 1.28194 ( 78) hydrogen bonds : bond 0.04271 ( 905) hydrogen bonds : angle 5.30290 ( 2493) Misc. bond : bond 0.00031 ( 3) link_BETA1-4 : bond 0.00740 ( 24) link_BETA1-4 : angle 2.94743 ( 72) link_NAG-ASN : bond 0.00671 ( 41) link_NAG-ASN : angle 3.78402 ( 123) *********************** 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 154 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 102 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: B 1029 MET cc_start: 0.8831 (tpp) cc_final: 0.8582 (tpp) REVERT: B 1038 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8640 (tptt) REVERT: A 495 TYR cc_start: 0.6675 (OUTLIER) cc_final: 0.4628 (m-10) REVERT: A 511 VAL cc_start: 0.8447 (OUTLIER) cc_final: 0.8213 (t) REVERT: A 731 MET cc_start: 0.8852 (ppp) cc_final: 0.8222 (ppp) REVERT: C 128 ILE cc_start: 0.8862 (mm) cc_final: 0.8481 (tp) REVERT: C 583 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7281 (pm20) REVERT: C 613 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8053 (pp30) REVERT: C 867 ASP cc_start: 0.7919 (p0) cc_final: 0.7566 (p0) REVERT: C 976 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8359 (m) REVERT: C 994 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8064 (t70) REVERT: C 1031 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7278 (mt-10) REVERT: C 1145 LEU cc_start: 0.4225 (OUTLIER) cc_final: 0.3659 (tp) outliers start: 52 outliers final: 27 residues processed: 145 average time/residue: 0.1455 time to fit residues: 37.0629 Evaluate side-chains 128 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 525 CYS Chi-restraints excluded: chain B residue 630 THR Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain A residue 22 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 495 TYR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 866 THR 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 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 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 295 optimal weight: 5.9990 chunk 18 optimal weight: 0.0040 chunk 35 optimal weight: 1.9990 chunk 315 optimal weight: 2.9990 chunk 201 optimal weight: 0.9980 chunk 290 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 310 optimal weight: 0.6980 chunk 230 optimal weight: 5.9990 chunk 102 optimal weight: 0.0670 chunk 141 optimal weight: 9.9990 overall best weight: 0.4930 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** C 115 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 895 GLN C 935 GLN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.106654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.081121 restraints weight = 107883.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079908 restraints weight = 77382.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.080381 restraints weight = 64718.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.080629 restraints weight = 57612.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080737 restraints weight = 52847.819| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27765 Z= 0.111 Angle : 0.673 19.823 37885 Z= 0.317 Chirality : 0.048 0.471 4447 Planarity : 0.004 0.079 4756 Dihedral : 10.604 108.267 5084 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 1.65 % Allowed : 17.98 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.15), residues: 3283 helix: 1.27 (0.21), residues: 664 sheet: 0.01 (0.22), residues: 573 loop : -2.02 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.021 0.001 TYR A 167 PHE 0.021 0.001 PHE A 183 TRP 0.018 0.001 TRP B 64 HIS 0.002 0.000 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00236 (27658) covalent geometry : angle 0.62664 (37612) SS BOND : bond 0.00234 ( 39) SS BOND : angle 1.16534 ( 78) hydrogen bonds : bond 0.03787 ( 905) hydrogen bonds : angle 5.08432 ( 2493) Misc. bond : bond 0.00016 ( 3) link_BETA1-4 : bond 0.00768 ( 24) link_BETA1-4 : angle 2.87335 ( 72) link_NAG-ASN : bond 0.00703 ( 41) link_NAG-ASN : angle 3.70140 ( 123) *********************** 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 161 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 113 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: B 1038 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8541 (tptt) REVERT: A 167 TYR cc_start: 0.8043 (t80) cc_final: 0.7817 (t80) REVERT: A 461 LEU cc_start: 0.7024 (OUTLIER) cc_final: 0.6079 (tp) REVERT: A 495 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.4308 (m-10) REVERT: A 731 MET cc_start: 0.8868 (ppp) cc_final: 0.8189 (ppp) REVERT: C 128 ILE cc_start: 0.8879 (mm) cc_final: 0.8504 (tp) REVERT: C 583 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7322 (pm20) REVERT: C 613 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8060 (pp30) REVERT: C 731 MET cc_start: 0.8715 (ppp) cc_final: 0.8415 (ppp) REVERT: C 763 LEU cc_start: 0.9260 (mt) cc_final: 0.9057 (pp) REVERT: C 867 ASP cc_start: 0.7904 (p0) cc_final: 0.7545 (p0) REVERT: C 976 VAL cc_start: 0.8545 (OUTLIER) cc_final: 0.8341 (m) REVERT: C 994 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7906 (t70) REVERT: C 1031 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7352 (mt-10) REVERT: C 1145 LEU cc_start: 0.4440 (OUTLIER) cc_final: 0.3678 (tp) outliers start: 48 outliers final: 29 residues processed: 153 average time/residue: 0.1544 time to fit residues: 41.0420 Evaluate side-chains 136 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.989 ------------------------------------------------------------------------------- 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 630 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 1066 THR Chi-restraints excluded: chain B residue 1104 VAL 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 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 495 TYR 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 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 827 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP 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 326 optimal weight: 7.9990 chunk 271 optimal weight: 10.0000 chunk 190 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 241 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 297 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 202 optimal weight: 5.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.106080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.081339 restraints weight = 118473.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.080911 restraints weight = 74347.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.081237 restraints weight = 66289.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.081495 restraints weight = 57727.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.081484 restraints weight = 52662.127| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27765 Z= 0.192 Angle : 0.741 19.394 37885 Z= 0.353 Chirality : 0.048 0.419 4447 Planarity : 0.004 0.077 4756 Dihedral : 10.627 111.575 5084 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 1.79 % Allowed : 18.53 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.14), residues: 3283 helix: 1.04 (0.21), residues: 668 sheet: -0.30 (0.21), residues: 587 loop : -2.08 (0.13), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1000 TYR 0.021 0.001 TYR C1067 PHE 0.029 0.001 PHE A 759 TRP 0.017 0.001 TRP B 64 HIS 0.006 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00434 (27658) covalent geometry : angle 0.69617 (37612) SS BOND : bond 0.00313 ( 39) SS BOND : angle 1.25692 ( 78) hydrogen bonds : bond 0.04509 ( 905) hydrogen bonds : angle 5.37132 ( 2493) Misc. bond : bond 0.00033 ( 3) link_BETA1-4 : bond 0.00622 ( 24) link_BETA1-4 : angle 3.01459 ( 72) link_NAG-ASN : bond 0.00761 ( 41) link_NAG-ASN : angle 3.84271 ( 123) *********************** 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 147 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 95 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8408 (mm) REVERT: A 167 TYR cc_start: 0.7998 (t80) cc_final: 0.7797 (t80) REVERT: A 495 TYR cc_start: 0.6709 (OUTLIER) cc_final: 0.4608 (m-10) REVERT: C 128 ILE cc_start: 0.8909 (mm) cc_final: 0.8552 (tp) REVERT: C 583 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7320 (pm20) REVERT: C 613 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8253 (pp30) REVERT: C 867 ASP cc_start: 0.8060 (p0) cc_final: 0.7698 (p0) REVERT: C 994 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8208 (t70) REVERT: C 1031 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7567 (mt-10) REVERT: C 1145 LEU cc_start: 0.4426 (OUTLIER) cc_final: 0.3753 (tp) outliers start: 52 outliers final: 36 residues processed: 141 average time/residue: 0.1411 time to fit residues: 35.2203 Evaluate side-chains 134 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 869 MET Chi-restraints excluded: chain B residue 1066 THR 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 127 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 877 LEU 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 906 PHE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 204 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 316 optimal weight: 0.9980 chunk 267 optimal weight: 6.9990 chunk 237 optimal weight: 5.9990 chunk 174 optimal weight: 0.5980 chunk 314 optimal weight: 0.3980 chunk 182 optimal weight: 1.9990 chunk 296 optimal weight: 7.9990 chunk 120 optimal weight: 0.5980 chunk 240 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 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 C1101 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.105059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.079458 restraints weight = 108484.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.078511 restraints weight = 78067.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.078849 restraints weight = 64298.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.079103 restraints weight = 58097.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.079254 restraints weight = 52725.073| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27765 Z= 0.119 Angle : 0.693 19.894 37885 Z= 0.325 Chirality : 0.047 0.429 4447 Planarity : 0.004 0.078 4756 Dihedral : 10.194 110.002 5084 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.69 % Allowed : 18.49 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 3283 helix: 1.19 (0.21), residues: 671 sheet: -0.10 (0.22), residues: 572 loop : -2.03 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.019 0.001 TYR B 636 PHE 0.017 0.001 PHE A 219 TRP 0.018 0.001 TRP B 64 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00263 (27658) covalent geometry : angle 0.64669 (37612) SS BOND : bond 0.00246 ( 39) SS BOND : angle 1.08459 ( 78) hydrogen bonds : bond 0.03996 ( 905) hydrogen bonds : angle 5.16603 ( 2493) Misc. bond : bond 0.00015 ( 3) link_BETA1-4 : bond 0.00757 ( 24) link_BETA1-4 : angle 2.90158 ( 72) link_NAG-ASN : bond 0.00709 ( 41) link_NAG-ASN : angle 3.78047 ( 123) ********************** 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 153 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 104 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: B 387 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8467 (mm) REVERT: B 774 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8465 (tp-100) REVERT: B 1038 LYS cc_start: 0.8859 (mmmt) cc_final: 0.8532 (tptt) REVERT: A 167 TYR cc_start: 0.8034 (t80) cc_final: 0.7791 (t80) REVERT: A 219 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8110 (t80) REVERT: A 495 TYR cc_start: 0.6418 (OUTLIER) cc_final: 0.4472 (m-10) REVERT: A 731 MET cc_start: 0.8850 (ppp) cc_final: 0.8177 (ppp) REVERT: C 128 ILE cc_start: 0.8888 (mm) cc_final: 0.8520 (tp) REVERT: C 583 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7333 (pm20) REVERT: C 613 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8188 (pp30) REVERT: C 731 MET cc_start: 0.8741 (ppp) cc_final: 0.8390 (ppp) REVERT: C 867 ASP cc_start: 0.7926 (p0) cc_final: 0.7561 (p0) REVERT: C 994 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8031 (t70) REVERT: C 1031 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7072 (mt-10) REVERT: C 1145 LEU cc_start: 0.4446 (OUTLIER) cc_final: 0.3716 (tp) outliers start: 49 outliers final: 34 residues processed: 145 average time/residue: 0.1377 time to fit residues: 34.8924 Evaluate side-chains 140 residues out of total 2913 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 99 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 869 MET Chi-restraints excluded: chain B residue 1066 THR 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 127 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 500 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 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 729 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 977 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 329 random chunks: chunk 254 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 37 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 281 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 242 optimal weight: 0.9990 chunk 79 optimal weight: 0.3980 chunk 298 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 312 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN ** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 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 895 GLN C 935 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.104428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.079471 restraints weight = 110362.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.078549 restraints weight = 71222.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.078997 restraints weight = 62744.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.079488 restraints weight = 53585.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.079512 restraints weight = 48738.485| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2254 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= 0.115 Angle : 0.675 19.891 37885 Z= 0.317 Chirality : 0.047 0.422 4447 Planarity : 0.004 0.078 4756 Dihedral : 9.510 110.362 5084 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.48 % Allowed : 18.87 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.15), residues: 3283 helix: 1.23 (0.21), residues: 671 sheet: -0.03 (0.21), residues: 609 loop : -1.99 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 210 TYR 0.018 0.001 TYR A 167 PHE 0.017 0.001 PHE A 400 TRP 0.016 0.001 TRP B 64 HIS 0.002 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00255 (27658) covalent geometry : angle 0.62797 (37612) SS BOND : bond 0.00232 ( 39) SS BOND : angle 1.00699 ( 78) hydrogen bonds : bond 0.03782 ( 905) hydrogen bonds : angle 5.05829 ( 2493) Misc. bond : bond 0.00013 ( 3) link_BETA1-4 : bond 0.00706 ( 24) link_BETA1-4 : angle 2.88096 ( 72) link_NAG-ASN : bond 0.00731 ( 41) link_NAG-ASN : angle 3.79266 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3831.21 seconds wall clock time: 67 minutes 43.36 seconds (4063.36 seconds total)