Starting phenix.real_space_refine on Sun Sep 13 22:36:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cs0_7578/09_2026/6cs0_7578.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cs0_7578/09_2026/6cs0_7578.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6cs0_7578/09_2026/6cs0_7578.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cs0_7578/09_2026/6cs0_7578.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cs0_7578/09_2026/6cs0_7578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cs0_7578/09_2026/6cs0_7578.map" model { file = "/net/cci-nas-00/data/ceres_data/6cs0_7578/09_2026/6cs0_7578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cs0_7578/09_2026/6cs0_7578.cif" } resolution = 3.8 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= 0.007 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 138 5.16 5 C 16490 2.51 5 N 4191 2.21 5 O 5090 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25909 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8339 Classifications: {'peptide': 1068} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1014} Chain breaks: 6 Chain: "B" Number of atoms: 8342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8342 Classifications: {'peptide': 1068} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1014} Chain breaks: 6 Chain: "C" Number of atoms: 8343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1069, 8343 Classifications: {'peptide': 1069} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1015} Chain breaks: 6 Chain: "D" 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 chiralities: 3 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" 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 chiralities: 3 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 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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 3 Chain: "K" 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 chiralities: 3 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 chiralities: 2 Chain: "M" 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 chiralities: 3 Chain: "N" 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 chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "R" 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 chiralities: 3 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "T" 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 chiralities: 3 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 chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.95, per 1000 atoms: 0.23 Number of scatterers: 25909 At special positions: 0 Unit cell: (147.29, 144.2, 177.16, 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 138 16.00 O 5090 8.00 N 4191 7.00 C 16490 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.05 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.04 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.02 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.03 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.01 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.02 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.04 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.02 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.02 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.04 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.02 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.02 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.02 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.02 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.03 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.02 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " ALPHA1-6 " BMA S 3 " - " MAN S 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1305 " - " ASN A 589 " " NAG A1310 " - " ASN A 691 " " NAG A1316 " - " ASN A1056 " " NAG B1301 " - " ASN B 65 " " NAG B1308 " - " ASN B 589 " " NAG B1311 " - " ASN B 691 " " NAG B1320 " - " ASN B1080 " " NAG B1321 " - " ASN B1116 " " NAG C1301 " - " ASN C 65 " " NAG C1304 " - " ASN C 227 " " NAG C1307 " - " ASN C 318 " " NAG C1308 " - " ASN C 589 " " NAG C1312 " - " ASN C 691 " " NAG C1320 " - " ASN C1056 " " NAG D 1 " - " ASN A 269 " " NAG E 1 " - " ASN A 602 " " NAG F 1 " - " ASN A 699 " " NAG G 1 " - " ASN A 783 " " NAG H 1 " - " ASN A1080 " " NAG I 1 " - " ASN A1116 " " NAG J 1 " - " ASN B 269 " " NAG K 1 " - " ASN B 318 " " NAG L 1 " - " ASN B 602 " " NAG M 1 " - " ASN B 699 " " NAG N 1 " - " ASN B 783 " " NAG O 1 " - " ASN B1056 " " NAG P 1 " - " ASN C 119 " " NAG Q 1 " - " ASN C 269 " " NAG R 1 " - " ASN C 602 " " NAG S 1 " - " ASN C 699 " " NAG T 1 " - " ASN C 783 " " NAG U 1 " - " ASN C1080 " " NAG V 1 " - " ASN C1116 " Time building additional restraints: 2.38 Conformation dependent library (CDL) restraints added in 1.2 seconds 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6004 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 52 sheets defined 22.0% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.582A pdb=" N GLU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.806A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 4.283A pdb=" N TYR A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.863A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 376 " --> pdb=" O LYS A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.589A pdb=" N TYR A 491 " --> pdb=" O GLY A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.606A pdb=" N THR A 608 " --> pdb=" O THR A 604 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS A 611 " --> pdb=" O SER A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 724 Processing helix chain 'A' and resid 731 through 736 removed outlier: 3.790A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.937A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN A 746 " --> pdb=" O CYS A 742 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 755 " --> pdb=" O GLY A 751 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N THR A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 763 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 809 removed outlier: 3.840A pdb=" N LEU A 803 " --> pdb=" O PHE A 799 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 removed outlier: 3.570A pdb=" N THR A 856 " --> pdb=" O ILE A 852 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 858 " --> pdb=" O ALA A 854 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 859 " --> pdb=" O TYR A 855 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 860 " --> pdb=" O THR A 856 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 873 removed outlier: 4.090A pdb=" N GLY A 871 " --> pdb=" O GLY A 867 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.095A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 920 removed outlier: 3.649A pdb=" N ALA A 912 " --> pdb=" O GLN A 908 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A 914 " --> pdb=" O ASN A 910 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 916 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU A 918 " --> pdb=" O SER A 914 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.519A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 941 " --> pdb=" O ASN A 937 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 947 " --> pdb=" O THR A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 removed outlier: 4.069A pdb=" N SER A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1013 removed outlier: 3.658A pdb=" N GLU A 972 " --> pdb=" O PRO A 968 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 985 " --> pdb=" O GLY A 981 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 986 " --> pdb=" O ARG A 982 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 988 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE A1000 " --> pdb=" O ARG A 996 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A1009 " --> pdb=" O ASN A1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.826A pdb=" N CYS B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 289 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.035A pdb=" N ASP B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 430 Processing helix chain 'B' and resid 488 through 492 removed outlier: 3.584A pdb=" N TYR B 491 " --> pdb=" O GLY B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.552A pdb=" N THR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 609 " --> pdb=" O ASP B 605 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N HIS B 611 " --> pdb=" O SER B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 739 removed outlier: 4.127A pdb=" N ALA B 732 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLN B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR B 738 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.634A pdb=" N ALA B 753 " --> pdb=" O LEU B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 765 removed outlier: 3.855A pdb=" N ARG B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 809 removed outlier: 3.659A pdb=" N LEU B 803 " --> pdb=" O PHE B 799 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 867 removed outlier: 3.548A pdb=" N GLY B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR B 863 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 873 Processing helix chain 'B' and resid 879 through 891 removed outlier: 3.582A pdb=" N TYR B 886 " --> pdb=" O MET B 882 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 900 removed outlier: 3.941A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.513A pdb=" N SER B 914 " --> pdb=" O ASN B 910 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE B 916 " --> pdb=" O ALA B 912 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR B 923 " --> pdb=" O SER B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.645A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 940 " --> pdb=" O GLN B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 965 Processing helix chain 'B' and resid 967 through 997 removed outlier: 3.581A pdb=" N GLU B 972 " --> pdb=" O PRO B 968 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU B 978 " --> pdb=" O GLN B 974 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR B 989 " --> pdb=" O SER B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1004 Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.925A pdb=" N CYS C 288 " --> pdb=" O ALA C 284 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER C 289 " --> pdb=" O GLU C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 372 through 377 removed outlier: 3.944A pdb=" N LEU C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.900A pdb=" N ASP C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.962A pdb=" N TYR C 491 " --> pdb=" O GLY C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 612 removed outlier: 3.584A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 736 removed outlier: 3.588A pdb=" N ALA C 732 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN C 733 " --> pdb=" O THR C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.795A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 753 " --> pdb=" O LEU C 749 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE C 764 " --> pdb=" O THR C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.708A pdb=" N ASN C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 864 removed outlier: 3.598A pdb=" N VAL C 860 " --> pdb=" O THR C 856 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 873 removed outlier: 4.015A pdb=" N GLY C 871 " --> pdb=" O GLY C 867 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C 872 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 removed outlier: 3.909A pdb=" N TYR C 886 " --> pdb=" O MET C 882 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG C 887 " --> pdb=" O GLN C 883 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 888 " --> pdb=" O MET C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 removed outlier: 3.521A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 923 removed outlier: 4.106A pdb=" N ASN C 910 " --> pdb=" O ALA C 906 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA C 912 " --> pdb=" O GLN C 908 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER C 914 " --> pdb=" O ASN C 910 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR C 921 " --> pdb=" O GLN C 917 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR C 923 " --> pdb=" O SER C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.936A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 964 Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.626A pdb=" N GLU C 972 " --> pdb=" O PRO C 968 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 978 " --> pdb=" O GLN C 974 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR C 980 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 983 " --> pdb=" O ILE C 979 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C1012 " --> pdb=" O ALA C1008 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 7.705A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 87 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS A 180 " --> pdb=" O ILE A 203 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 35 removed outlier: 7.705A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 87 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 219 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.857A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.655A pdb=" N ASP A 57 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.593A pdb=" N GLY A 100 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP A 101 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG A 126 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 123 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR A 163 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 125 " --> pdb=" O PHE A 161 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N PHE A 161 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA A 127 " --> pdb=" O CYS A 159 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N CYS A 159 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ASN A 155 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 146 through 149 removed outlier: 3.715A pdb=" N THR A 146 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 615 through 616 removed outlier: 5.053A pdb=" N ILE A 299 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR A 585 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLN A 301 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 583 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N SER A 303 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 581 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N TYR A 598 " --> pdb=" O CYS A 635 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 314 removed outlier: 6.206A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 532 " --> pdb=" O PHE A 529 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.994A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS A 365 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 439 through 441 removed outlier: 3.666A pdb=" N TYR A 440 " --> pdb=" O ASN A 479 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 640 through 646 removed outlier: 4.942A pdb=" N THR A 678 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N THR A 644 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.444A pdb=" N ALA A 683 " --> pdb=" O MET B 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 710 removed outlier: 3.705A pdb=" N SER A 703 " --> pdb=" O THR A1048 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A1046 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU A1045 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A1033 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 699 through 710 removed outlier: 3.705A pdb=" N SER A 703 " --> pdb=" O THR A1048 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS A1046 " --> pdb=" O THR A 705 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 718 removed outlier: 4.218A pdb=" N LYS A 715 " --> pdb=" O LEU A 843 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AB8, first strand: chain 'A' and resid 1058 through 1060 removed outlier: 3.714A pdb=" N THR A1058 " --> pdb=" O PHE A1079 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A1076 " --> pdb=" O THR A1087 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR A1087 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 3.959A pdb=" N SER A1105 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS A1068 " --> pdb=" O HIS A1065 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A1062 " --> pdb=" O ILE A1115 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.566A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR B 252 " --> pdb=" O PHE B 69 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS B 180 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 186 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 196 " --> pdb=" O PHE B 220 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.566A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR B 252 " --> pdb=" O PHE B 69 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.652A pdb=" N ASP B 57 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR B 260 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL B 276 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 81 through 82 removed outlier: 5.771A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.717A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.533A pdb=" N TYR B 300 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 636 " --> pdb=" O PHE B 629 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 312 through 314 removed outlier: 6.687A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLY B 534 " --> pdb=" O PHE B 527 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASP B 560 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.570A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP B 385 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 421 " --> pdb=" O VAL B 497 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N CYS B 419 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.036A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AD2, first strand: chain 'B' and resid 640 through 646 removed outlier: 5.855A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N VAL B 642 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS B 661 " --> pdb=" O SER B 673 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.114A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 693 through 696 removed outlier: 3.509A pdb=" N ARG B1055 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B1076 " --> pdb=" O THR B1087 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B1087 " --> pdb=" O VAL B1076 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N GLN B1088 " --> pdb=" O SER B1093 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER B1093 " --> pdb=" O GLN B1088 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 709 removed outlier: 4.018A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B1048 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU B1045 " --> pdb=" O SER B1033 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER B1033 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 701 through 709 removed outlier: 4.018A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B1048 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B1041 " --> pdb=" O ALA B1038 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 717 through 718 Processing sheet with id=AD8, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD9, first strand: chain 'B' and resid 821 through 822 Processing sheet with id=AE1, first strand: chain 'B' and resid 1102 through 1104 removed outlier: 3.773A pdb=" N HIS B1065 " --> pdb=" O LYS B1068 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B1070 " --> pdb=" O ILE B1063 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B1063 " --> pdb=" O TYR B1070 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 32 through 35 removed outlier: 3.630A pdb=" N SER C 64 " --> pdb=" O SER C 35 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR C 67 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL C 254 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C 188 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N TYR C 200 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C 215 " --> pdb=" O TYR C 200 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG C 38 " --> pdb=" O ASN C 214 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N LEU C 216 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL C 40 " --> pdb=" O LEU C 216 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.612A pdb=" N THR C 260 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.612A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 137 through 140 removed outlier: 6.861A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 298 through 301 removed outlier: 3.503A pdb=" N GLY C 298 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 582 " --> pdb=" O LEU C 597 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 578 through 579 removed outlier: 3.752A pdb=" N GLY C 579 " --> pdb=" O PHE C 305 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.887A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 439 through 441 removed outlier: 3.503A pdb=" N ASN C 479 " --> pdb=" O TYR C 440 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 640 through 646 removed outlier: 4.284A pdb=" N THR C 678 " --> pdb=" O VAL C 642 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR C 644 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 693 through 697 removed outlier: 3.563A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 700 through 710 removed outlier: 3.525A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AF5, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF6, first strand: chain 'C' and resid 822 through 823 removed outlier: 3.506A pdb=" N LEU C 823 " --> pdb=" O ILE C 832 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 3.972A pdb=" N SER C1105 " --> pdb=" O ALA C1069 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA C1062 " --> pdb=" O ILE C1115 " (cutoff:3.500A) 872 hydrogen bonds defined for protein. 2379 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: 7.05 Time building geometry restraints manager: 3.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8129 1.34 - 1.47: 7056 1.47 - 1.60: 11134 1.60 - 1.73: 0 1.73 - 1.86: 186 Bond restraints: 26505 Sorted by residual: bond pdb=" C LYS C 142 " pdb=" N PRO C 143 " ideal model delta sigma weight residual 1.336 1.387 -0.052 9.80e-03 1.04e+04 2.77e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 8.86e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" C1 MAN S 4 " pdb=" C2 MAN S 4 " ideal model delta sigma weight residual 1.526 1.578 -0.052 2.00e-02 2.50e+03 6.65e+00 bond pdb=" C VAL C 842 " pdb=" N LEU C 843 " ideal model delta sigma weight residual 1.331 1.264 0.067 2.83e-02 1.25e+03 5.60e+00 ... (remaining 26500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 35288 2.90 - 5.80: 705 5.80 - 8.71: 59 8.71 - 11.61: 8 11.61 - 14.51: 2 Bond angle restraints: 36062 Sorted by residual: angle pdb=" C TYR B1070 " pdb=" N PHE B1071 " pdb=" CA PHE B1071 " ideal model delta sigma weight residual 121.61 136.12 -14.51 1.39e+00 5.18e-01 1.09e+02 angle pdb=" C PHE B 83 " pdb=" N LYS B 84 " pdb=" CA LYS B 84 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.49e+01 angle pdb=" N PRO A 968 " pdb=" CA PRO A 968 " pdb=" C PRO A 968 " ideal model delta sigma weight residual 110.70 116.55 -5.85 1.22e+00 6.72e-01 2.30e+01 angle pdb=" C PHE C 83 " pdb=" N LYS C 84 " pdb=" CA LYS C 84 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.27e+01 angle pdb=" C ARG B 207 " pdb=" N ASP B 208 " pdb=" CA ASP B 208 " ideal model delta sigma weight residual 120.82 127.95 -7.13 1.50e+00 4.44e-01 2.26e+01 ... (remaining 36057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 14599 17.07 - 34.14: 542 34.14 - 51.22: 87 51.22 - 68.29: 9 68.29 - 85.36: 7 Dihedral angle restraints: 15244 sinusoidal: 5910 harmonic: 9334 Sorted by residual: dihedral pdb=" CB CYS B 822 " pdb=" SG CYS B 822 " pdb=" SG CYS B 833 " pdb=" CB CYS B 833 " ideal model delta sinusoidal sigma weight residual 93.00 7.64 85.36 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CB CYS A1014 " pdb=" SG CYS A1014 " pdb=" SG CYS A1025 " pdb=" CB CYS A1025 " ideal model delta sinusoidal sigma weight residual -86.00 -166.74 80.74 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS C 323 " pdb=" SG CYS C 323 " pdb=" SG CYS C 348 " pdb=" CB CYS C 348 " ideal model delta sinusoidal sigma weight residual -86.00 -160.36 74.36 1 1.00e+01 1.00e-02 7.01e+01 ... (remaining 15241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3668 0.086 - 0.173: 552 0.173 - 0.259: 19 0.259 - 0.346: 18 0.346 - 0.432: 7 Chirality restraints: 4264 Sorted by residual: chirality pdb=" C1 NAG T 1 " pdb=" ND2 ASN C 783 " pdb=" C2 NAG T 1 " pdb=" O5 NAG T 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CB ILE A 72 " pdb=" CA ILE A 72 " pdb=" CG1 ILE A 72 " pdb=" CG2 ILE A 72 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN C1116 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 4261 not shown) Planarity restraints: 4603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 22 " -0.016 2.00e-02 2.50e+03 2.23e-02 8.73e+00 pdb=" CG PHE C 22 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE C 22 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 PHE C 22 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE C 22 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 22 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 22 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 968 " 0.049 5.00e-02 4.00e+02 7.37e-02 8.70e+00 pdb=" N PRO C 969 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 969 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 969 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A1060 " -0.049 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO A1061 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A1061 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1061 " -0.040 5.00e-02 4.00e+02 ... (remaining 4600 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5827 2.78 - 3.31: 22718 3.31 - 3.84: 43386 3.84 - 4.37: 50641 4.37 - 4.90: 84270 Nonbonded interactions: 206842 Sorted by model distance: nonbonded pdb=" OD2 ASP C 564 " pdb=" OG1 THR C 567 " model vdw 2.254 3.040 nonbonded pdb=" OG SER B 690 " pdb=" OD1 ASN B 692 " model vdw 2.267 3.040 nonbonded pdb=" O GLN A 917 " pdb=" OG1 THR A 921 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR A 425 " pdb=" O PRO A 493 " model vdw 2.268 3.040 nonbonded pdb=" OH TYR B 738 " pdb=" OG1 THR B 980 " model vdw 2.269 3.040 ... (remaining 206837 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 18 through 366 or resid 371 through 823 or resid 831 throu \ gh 1316)) selection = (chain 'B' and (resid 18 through 366 or resid 371 through 662 or resid 672 throu \ gh 1320)) selection = (chain 'C' and (resid 18 through 823 or resid 831 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'R' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'Q' 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: 2.890 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.850 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 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 : 0.007 0.076 26616 Z= 0.321 Angle : 1.038 14.511 36350 Z= 0.547 Chirality : 0.062 0.432 4264 Planarity : 0.007 0.074 4569 Dihedral : 9.263 76.584 9105 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 0.04 % Allowed : 0.72 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -4.10 (0.12), residues: 3163 helix: -3.93 (0.12), residues: 621 sheet: -1.60 (0.20), residues: 603 loop : -2.79 (0.12), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 99 TYR 0.031 0.003 TYR C 42 PHE 0.050 0.004 PHE C 22 TRP 0.037 0.003 TRP B 423 HIS 0.012 0.002 HIS B1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.32 (26505) covalent geometry : angle 1.00924 / 0.54 (36062) SS BOND : bond 0.00691 / 0.45 ( 45) SS BOND : angle 2.26278 / 1.50 ( 90) hydrogen bonds : bond 0.29573 / 19.63 ( 819) hydrogen bonds : angle 11.26271 / 7.79 ( 2379) link_ALPHA1-3 : bond 0.00620 / 0.33 ( 1) link_ALPHA1-3 : angle 1.30858 / 0.73 ( 3) link_ALPHA1-6 : bond 0.00151 / 0.08 ( 1) link_ALPHA1-6 : angle 1.66526 / 0.92 ( 3) link_BETA1-4 : bond 0.00866 / 0.66 ( 30) link_BETA1-4 : angle 2.70996 / 1.84 ( 90) link_NAG-ASN : bond 0.00602 / 0.41 ( 34) link_NAG-ASN : angle 3.59708 / 2.39 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 446 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TRP cc_start: 0.6327 (m-90) cc_final: 0.5611 (m-90) REVERT: A 245 TRP cc_start: 0.2737 (m100) cc_final: 0.1962 (m-90) REVERT: A 302 THR cc_start: 0.9344 (t) cc_final: 0.9116 (m) REVERT: B 230 ASN cc_start: 0.5756 (m-40) cc_final: 0.5257 (m-40) REVERT: B 263 MET cc_start: 0.6450 (ttm) cc_final: 0.6243 (ttp) REVERT: B 375 ASN cc_start: 0.7515 (m-40) cc_final: 0.7292 (t0) REVERT: B 944 LEU cc_start: 0.8505 (tp) cc_final: 0.8294 (tp) REVERT: B 996 ARG cc_start: 0.7189 (ttm110) cc_final: 0.6922 (ttm110) REVERT: B 1033 SER cc_start: 0.6998 (t) cc_final: 0.6778 (t) REVERT: B 1114 ILE cc_start: 0.5762 (tt) cc_final: 0.5546 (tt) REVERT: C 144 MET cc_start: 0.5475 (mtp) cc_final: 0.3372 (tmm) REVERT: C 346 SER cc_start: 0.7873 (t) cc_final: 0.7571 (p) REVERT: C 1079 PHE cc_start: 0.4127 (t80) cc_final: 0.3832 (t80) outliers start: 1 outliers final: 1 residues processed: 447 average time/residue: 0.1834 time to fit residues: 125.5901 Evaluate side-chains 226 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 225 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 708 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 112 GLN A 230 ASN A 733 ASN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 936 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1117 ASN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN B 641 HIS B 786 GLN B1065 HIS ** B1088 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 HIS ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN C 746 ASN C 889 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.144578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.122030 restraints weight = 105206.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.120321 restraints weight = 99876.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.120709 restraints weight = 82603.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.120988 restraints weight = 67893.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.121256 restraints weight = 61942.959| |-----------------------------------------------------------------------------| r_work (final): 0.4018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 26616 Z= 0.217 Angle : 0.776 9.791 36350 Z= 0.405 Chirality : 0.049 0.282 4264 Planarity : 0.006 0.068 4569 Dihedral : 6.806 40.605 3439 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 1.55 % Allowed : 6.65 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.13), residues: 3163 helix: -2.60 (0.16), residues: 641 sheet: -1.18 (0.20), residues: 665 loop : -2.53 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 996 TYR 0.018 0.002 TYR B1070 PHE 0.023 0.002 PHE C 83 TRP 0.017 0.002 TRP B 423 HIS 0.006 0.001 HIS A1040 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (26505) covalent geometry : angle 0.75735 / 0.40 (36062) SS BOND : bond 0.00739 / 0.45 ( 45) SS BOND : angle 1.74221 / 1.13 ( 90) hydrogen bonds : bond 0.05917 / 3.89 ( 819) hydrogen bonds : angle 7.48584 / 5.18 ( 2379) link_ALPHA1-3 : bond 0.00501 / 0.26 ( 1) link_ALPHA1-3 : angle 1.80940 / 1.01 ( 3) link_ALPHA1-6 : bond 0.00407 / 0.21 ( 1) link_ALPHA1-6 : angle 1.78368 / 0.98 ( 3) link_BETA1-4 : bond 0.00482 / 0.35 ( 30) link_BETA1-4 : angle 1.84618 / 1.28 ( 90) link_NAG-ASN : bond 0.00369 / 0.25 ( 34) link_NAG-ASN : angle 2.46762 / 1.73 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 268 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TRP cc_start: 0.5489 (m-90) cc_final: 0.5198 (m-90) REVERT: A 245 TRP cc_start: 0.2423 (m100) cc_final: 0.1958 (m-90) REVERT: A 755 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6060 (mm-30) REVERT: A 1120 TYR cc_start: 0.6676 (m-10) cc_final: 0.6147 (t80) REVERT: B 375 ASN cc_start: 0.7675 (m-40) cc_final: 0.6979 (t0) REVERT: B 620 ARG cc_start: 0.7358 (mmp80) cc_final: 0.7049 (mmp80) REVERT: B 896 ASN cc_start: 0.7399 (m-40) cc_final: 0.7117 (m-40) REVERT: B 1013 GLU cc_start: 0.5118 (mm-30) cc_final: 0.4436 (mm-30) REVERT: C 144 MET cc_start: 0.5085 (mtp) cc_final: 0.3269 (tmm) REVERT: C 346 SER cc_start: 0.8136 (t) cc_final: 0.7882 (p) REVERT: C 722 MET cc_start: 0.8155 (mmm) cc_final: 0.7174 (tmm) REVERT: C 985 SER cc_start: 0.9170 (m) cc_final: 0.8935 (p) outliers start: 43 outliers final: 27 residues processed: 300 average time/residue: 0.1608 time to fit residues: 78.3157 Evaluate side-chains 239 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 1032 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 154 optimal weight: 5.9990 chunk 206 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 119 optimal weight: 40.0000 chunk 253 optimal weight: 10.0000 chunk 79 optimal weight: 0.0980 chunk 34 optimal weight: 0.3980 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 0.0970 chunk 300 optimal weight: 3.9990 chunk 184 optimal weight: 7.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 661 HIS ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 904 GLN B 907 ASN B 974 GLN B1088 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.146051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.123449 restraints weight = 105464.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.122379 restraints weight = 110978.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.122926 restraints weight = 80032.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.123152 restraints weight = 67883.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.123361 restraints weight = 61259.626| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26616 Z= 0.131 Angle : 0.646 8.879 36350 Z= 0.335 Chirality : 0.046 0.267 4264 Planarity : 0.005 0.059 4569 Dihedral : 5.960 32.831 3439 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 2.01 % Allowed : 7.23 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.79 (0.14), residues: 3163 helix: -1.61 (0.19), residues: 643 sheet: -1.02 (0.19), residues: 668 loop : -2.35 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 395 TYR 0.021 0.001 TYR B 163 PHE 0.027 0.002 PHE A 83 TRP 0.014 0.001 TRP B1084 HIS 0.004 0.001 HIS A1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (26505) covalent geometry : angle 0.63018 / 0.33 (36062) SS BOND : bond 0.00403 / 0.28 ( 45) SS BOND : angle 1.42875 / 0.92 ( 90) hydrogen bonds : bond 0.04368 / 2.87 ( 819) hydrogen bonds : angle 6.56031 / 4.55 ( 2379) link_ALPHA1-3 : bond 0.00718 / 0.38 ( 1) link_ALPHA1-3 : angle 1.53158 / 0.86 ( 3) link_ALPHA1-6 : bond 0.00521 / 0.27 ( 1) link_ALPHA1-6 : angle 1.60489 / 0.90 ( 3) link_BETA1-4 : bond 0.00500 / 0.37 ( 30) link_BETA1-4 : angle 1.54424 / 1.06 ( 90) link_NAG-ASN : bond 0.00343 / 0.25 ( 34) link_NAG-ASN : angle 2.01053 / 1.39 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 268 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 ASN cc_start: 0.7748 (p0) cc_final: 0.7365 (p0) REVERT: A 1120 TYR cc_start: 0.6346 (m-10) cc_final: 0.6145 (t80) REVERT: B 619 TRP cc_start: 0.7760 (m-90) cc_final: 0.7300 (m-90) REVERT: B 679 MET cc_start: 0.6454 (ptp) cc_final: 0.6176 (ptt) REVERT: B 759 ASN cc_start: 0.7864 (m-40) cc_final: 0.7556 (m-40) REVERT: B 1013 GLU cc_start: 0.4279 (mm-30) cc_final: 0.3745 (mm-30) REVERT: C 144 MET cc_start: 0.5251 (mtp) cc_final: 0.3231 (tmm) REVERT: C 337 VAL cc_start: 0.5598 (OUTLIER) cc_final: 0.5321 (t) REVERT: C 346 SER cc_start: 0.7793 (t) cc_final: 0.7537 (p) REVERT: C 605 ASP cc_start: 0.7937 (m-30) cc_final: 0.7515 (t0) REVERT: C 984 GLN cc_start: 0.8281 (pp30) cc_final: 0.7742 (pp30) REVERT: C 985 SER cc_start: 0.8813 (m) cc_final: 0.8438 (p) REVERT: C 1001 ARG cc_start: 0.7346 (tmm-80) cc_final: 0.7066 (tmm-80) outliers start: 56 outliers final: 33 residues processed: 305 average time/residue: 0.1533 time to fit residues: 76.2963 Evaluate side-chains 242 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 837 PHE Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 947 GLN Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 1032 MET Chi-restraints excluded: chain C residue 1063 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 155 optimal weight: 3.9990 chunk 114 optimal weight: 20.0000 chunk 107 optimal weight: 0.3980 chunk 306 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 204 optimal weight: 0.7980 chunk 301 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 221 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 838 ASN A 908 GLN B 109 ASN B 149 HIS B 201 GLN B 896 ASN B 992 GLN C 29 ASN C1036 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.143727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.118332 restraints weight = 99435.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.118331 restraints weight = 79328.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.118413 restraints weight = 58362.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.118547 restraints weight = 61809.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.118783 restraints weight = 51266.206| |-----------------------------------------------------------------------------| r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 26616 Z= 0.145 Angle : 0.648 10.962 36350 Z= 0.334 Chirality : 0.045 0.260 4264 Planarity : 0.004 0.060 4569 Dihedral : 5.741 31.699 3439 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 2.70 % Allowed : 8.56 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.14), residues: 3163 helix: -1.11 (0.20), residues: 637 sheet: -0.96 (0.19), residues: 659 loop : -2.24 (0.13), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 306 TYR 0.018 0.001 TYR C 252 PHE 0.025 0.002 PHE B 83 TRP 0.016 0.001 TRP A 101 HIS 0.006 0.001 HIS C1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (26505) covalent geometry : angle 0.63178 / 0.33 (36062) SS BOND : bond 0.00477 / 0.22 ( 45) SS BOND : angle 1.70450 / 1.12 ( 90) hydrogen bonds : bond 0.04073 / 2.67 ( 819) hydrogen bonds : angle 6.31372 / 4.35 ( 2379) link_ALPHA1-3 : bond 0.00510 / 0.27 ( 1) link_ALPHA1-3 : angle 1.44125 / 0.82 ( 3) link_ALPHA1-6 : bond 0.00437 / 0.23 ( 1) link_ALPHA1-6 : angle 1.63808 / 0.91 ( 3) link_BETA1-4 : bond 0.00439 / 0.33 ( 30) link_BETA1-4 : angle 1.50928 / 1.04 ( 90) link_NAG-ASN : bond 0.00296 / 0.21 ( 34) link_NAG-ASN : angle 1.93486 / 1.34 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 223 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 ASP cc_start: 0.7349 (p0) cc_final: 0.7148 (p0) REVERT: A 942 ASN cc_start: 0.8361 (p0) cc_final: 0.8132 (p0) REVERT: A 1120 TYR cc_start: 0.6468 (m-10) cc_final: 0.6153 (t80) REVERT: B 263 MET cc_start: 0.6925 (ttm) cc_final: 0.6425 (ttp) REVERT: B 299 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8845 (pt) REVERT: B 417 MET cc_start: 0.4629 (OUTLIER) cc_final: 0.4327 (mmm) REVERT: B 620 ARG cc_start: 0.7250 (mmp80) cc_final: 0.6858 (mmp80) REVERT: B 679 MET cc_start: 0.6623 (ptp) cc_final: 0.6344 (ptt) REVERT: B 759 ASN cc_start: 0.8229 (m-40) cc_final: 0.7811 (m-40) REVERT: B 1013 GLU cc_start: 0.4617 (mm-30) cc_final: 0.3744 (mm-30) REVERT: B 1032 MET cc_start: 0.6608 (ttt) cc_final: 0.6197 (ttt) REVERT: C 50 ASP cc_start: 0.7336 (t0) cc_final: 0.7117 (t0) REVERT: C 144 MET cc_start: 0.4909 (mtp) cc_final: 0.3161 (tmm) REVERT: C 151 MET cc_start: 0.6337 (mmm) cc_final: 0.5875 (tpt) REVERT: C 346 SER cc_start: 0.8211 (t) cc_final: 0.7959 (p) REVERT: C 605 ASP cc_start: 0.8599 (m-30) cc_final: 0.7826 (t0) REVERT: C 736 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7309 (tp) REVERT: C 985 SER cc_start: 0.9156 (m) cc_final: 0.8889 (p) outliers start: 75 outliers final: 50 residues processed: 277 average time/residue: 0.1471 time to fit residues: 66.8888 Evaluate side-chains 251 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 198 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 838 ASN Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 837 PHE Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 903 LYS Chi-restraints excluded: chain C residue 1032 MET Chi-restraints excluded: chain C residue 1063 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 198 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 55 optimal weight: 9.9990 chunk 162 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 126 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 215 optimal weight: 7.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 974 GLN B1036 GLN C1030 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.141674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.117622 restraints weight = 100474.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.116234 restraints weight = 80695.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.116901 restraints weight = 63030.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.116999 restraints weight = 56510.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.117087 restraints weight = 51418.186| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 26616 Z= 0.184 Angle : 0.675 11.254 36350 Z= 0.346 Chirality : 0.047 0.273 4264 Planarity : 0.004 0.049 4569 Dihedral : 5.783 32.185 3439 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.91 % Allowed : 9.82 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.14), residues: 3163 helix: -1.01 (0.19), residues: 641 sheet: -0.90 (0.20), residues: 647 loop : -2.31 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 747 TYR 0.023 0.002 TYR B 383 PHE 0.030 0.002 PHE B 83 TRP 0.013 0.001 TRP A 101 HIS 0.005 0.001 HIS C 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (26505) covalent geometry : angle 0.66015 / 0.34 (36062) SS BOND : bond 0.00527 / 0.25 ( 45) SS BOND : angle 1.50387 / 0.97 ( 90) hydrogen bonds : bond 0.04171 / 2.70 ( 819) hydrogen bonds : angle 6.30558 / 4.35 ( 2379) link_ALPHA1-3 : bond 0.00516 / 0.27 ( 1) link_ALPHA1-3 : angle 1.45465 / 0.82 ( 3) link_ALPHA1-6 : bond 0.00378 / 0.20 ( 1) link_ALPHA1-6 : angle 1.69617 / 0.94 ( 3) link_BETA1-4 : bond 0.00503 / 0.38 ( 30) link_BETA1-4 : angle 1.49830 / 1.03 ( 90) link_NAG-ASN : bond 0.00343 / 0.25 ( 34) link_NAG-ASN : angle 2.01923 / 1.39 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 203 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 ASN cc_start: 0.8354 (p0) cc_final: 0.8055 (p0) REVERT: A 1120 TYR cc_start: 0.6680 (m-10) cc_final: 0.6243 (t80) REVERT: B 263 MET cc_start: 0.6846 (ttm) cc_final: 0.6505 (ttp) REVERT: B 299 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8781 (pt) REVERT: B 417 MET cc_start: 0.4852 (OUTLIER) cc_final: 0.4536 (mmm) REVERT: B 1013 GLU cc_start: 0.4495 (mm-30) cc_final: 0.3696 (mm-30) REVERT: B 1032 MET cc_start: 0.6492 (ttt) cc_final: 0.6074 (ttt) REVERT: C 50 ASP cc_start: 0.7307 (t0) cc_final: 0.7000 (t0) REVERT: C 107 MET cc_start: 0.2326 (mmt) cc_final: 0.2029 (mmm) REVERT: C 144 MET cc_start: 0.5182 (mtp) cc_final: 0.3197 (tmm) REVERT: C 151 MET cc_start: 0.6416 (mmm) cc_final: 0.6058 (tpt) REVERT: C 605 ASP cc_start: 0.8513 (m-30) cc_final: 0.7839 (t0) REVERT: C 694 ILE cc_start: 0.7373 (mt) cc_final: 0.7162 (mt) REVERT: C 984 GLN cc_start: 0.8706 (pp30) cc_final: 0.8115 (pp30) REVERT: C 985 SER cc_start: 0.9109 (m) cc_final: 0.8636 (p) outliers start: 81 outliers final: 58 residues processed: 260 average time/residue: 0.1534 time to fit residues: 66.1900 Evaluate side-chains 249 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain B residue 42 TYR Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 417 MET Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 837 PHE Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 903 LYS Chi-restraints excluded: chain C residue 1032 MET Chi-restraints excluded: chain C residue 1063 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 42 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 56 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 128 optimal weight: 20.0000 chunk 317 optimal weight: 6.9990 chunk 119 optimal weight: 10.0000 chunk 278 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 ASN A 818 GLN ** A 931 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1117 ASN B 147 GLN B 201 GLN B 630 GLN B 896 ASN B 951 ASN C 29 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN C 908 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.139412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.116651 restraints weight = 105634.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.113792 restraints weight = 94000.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.114259 restraints weight = 86213.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.114439 restraints weight = 74689.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.114569 restraints weight = 67116.168| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 26616 Z= 0.292 Angle : 0.836 12.014 36350 Z= 0.429 Chirality : 0.052 0.351 4264 Planarity : 0.005 0.054 4569 Dihedral : 6.510 44.211 3439 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 3.81 % Allowed : 10.07 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.89 (0.14), residues: 3163 helix: -1.45 (0.18), residues: 645 sheet: -1.02 (0.20), residues: 631 loop : -2.52 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 444 TYR 0.022 0.002 TYR A 256 PHE 0.038 0.003 PHE B 83 TRP 0.018 0.002 TRP B1084 HIS 0.012 0.002 HIS C 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.29 (26505) covalent geometry : angle 0.81860 / 0.43 (36062) SS BOND : bond 0.00483 / 0.31 ( 45) SS BOND : angle 1.92703 / 1.29 ( 90) hydrogen bonds : bond 0.04996 / 3.22 ( 819) hydrogen bonds : angle 6.98409 / 4.81 ( 2379) link_ALPHA1-3 : bond 0.00387 / 0.20 ( 1) link_ALPHA1-3 : angle 1.50219 / 0.86 ( 3) link_ALPHA1-6 : bond 0.00326 / 0.17 ( 1) link_ALPHA1-6 : angle 1.89504 / 1.05 ( 3) link_BETA1-4 : bond 0.00551 / 0.43 ( 30) link_BETA1-4 : angle 1.64921 / 1.14 ( 90) link_NAG-ASN : bond 0.00672 / 0.48 ( 34) link_NAG-ASN : angle 2.55034 / 1.74 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 190 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 942 ASN cc_start: 0.8528 (p0) cc_final: 0.8200 (p0) REVERT: A 1120 TYR cc_start: 0.6733 (m-10) cc_final: 0.6141 (t80) REVERT: B 263 MET cc_start: 0.7153 (ttm) cc_final: 0.6682 (ttp) REVERT: B 299 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8695 (pt) REVERT: B 1013 GLU cc_start: 0.4704 (mm-30) cc_final: 0.3987 (mm-30) REVERT: B 1032 MET cc_start: 0.6886 (ttt) cc_final: 0.6605 (ttt) REVERT: C 144 MET cc_start: 0.4471 (mtp) cc_final: 0.2963 (tmm) REVERT: C 151 MET cc_start: 0.6786 (mmm) cc_final: 0.6270 (tpt) REVERT: C 694 ILE cc_start: 0.7031 (mt) cc_final: 0.6804 (mt) REVERT: C 985 SER cc_start: 0.9209 (m) cc_final: 0.8830 (p) outliers start: 106 outliers final: 72 residues processed: 274 average time/residue: 0.1440 time to fit residues: 66.3848 Evaluate side-chains 253 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 180 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 721 ASN Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 850 ASP Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 933 VAL Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 837 PHE Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 878 ILE Chi-restraints excluded: chain B residue 883 GLN Chi-restraints excluded: chain B residue 905 ILE Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 263 MET Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 610 ILE Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 903 LYS Chi-restraints excluded: chain C residue 907 ASN Chi-restraints excluded: chain C residue 990 VAL Chi-restraints excluded: chain C residue 1032 MET Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1097 ILE Chi-restraints excluded: chain C residue 1112 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 63 optimal weight: 6.9990 chunk 270 optimal weight: 0.8980 chunk 41 optimal weight: 40.0000 chunk 95 optimal weight: 0.8980 chunk 224 optimal weight: 20.0000 chunk 209 optimal weight: 0.8980 chunk 271 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 630 GLN B 896 ASN B 908 GLN C 29 ASN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 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 = 0.4426 r_free = 0.4426 target = 0.141394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.116698 restraints weight = 96752.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.115248 restraints weight = 77251.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.115454 restraints weight = 68177.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.115620 restraints weight = 58889.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.116091 restraints weight = 51880.191| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 26616 Z= 0.138 Angle : 0.664 12.256 36350 Z= 0.340 Chirality : 0.047 0.367 4264 Planarity : 0.004 0.055 4569 Dihedral : 5.916 37.328 3439 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.30 % Allowed : 12.05 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.53 (0.14), residues: 3163 helix: -0.78 (0.20), residues: 634 sheet: -0.97 (0.20), residues: 627 loop : -2.36 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 747 TYR 0.019 0.001 TYR A 738 PHE 0.026 0.002 PHE B 83 TRP 0.021 0.002 TRP C 340 HIS 0.003 0.001 HIS B1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (26505) covalent geometry : angle 0.64918 / 0.34 (36062) SS BOND : bond 0.00322 / 0.21 ( 45) SS BOND : angle 1.46504 / 0.95 ( 90) hydrogen bonds : bond 0.03973 / 2.58 ( 819) hydrogen bonds : angle 6.37451 / 4.41 ( 2379) link_ALPHA1-3 : bond 0.00490 / 0.26 ( 1) link_ALPHA1-3 : angle 1.46880 / 0.81 ( 3) link_ALPHA1-6 : bond 0.00447 / 0.24 ( 1) link_ALPHA1-6 : angle 1.64699 / 0.91 ( 3) link_BETA1-4 : bond 0.00451 / 0.34 ( 30) link_BETA1-4 : angle 1.39309 / 0.95 ( 90) link_NAG-ASN : bond 0.00291 / 0.22 ( 34) link_NAG-ASN : angle 2.06248 / 1.41 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 213 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 800 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7396 (tp) REVERT: A 932 ASP cc_start: 0.7059 (p0) cc_final: 0.6757 (p0) REVERT: A 942 ASN cc_start: 0.8361 (p0) cc_final: 0.8095 (p0) REVERT: A 1120 TYR cc_start: 0.6453 (m-10) cc_final: 0.6170 (t80) REVERT: B 37 MET cc_start: 0.7351 (mmp) cc_final: 0.6944 (mmp) REVERT: B 263 MET cc_start: 0.6963 (ttm) cc_final: 0.6480 (ttp) REVERT: B 417 MET cc_start: 0.5016 (mmt) cc_final: 0.4424 (mmm) REVERT: B 884 MET cc_start: 0.7720 (mmm) cc_final: 0.7020 (mmm) REVERT: B 1013 GLU cc_start: 0.4432 (mm-30) cc_final: 0.3767 (mm-30) REVERT: B 1032 MET cc_start: 0.6408 (ttt) cc_final: 0.6073 (ttt) REVERT: C 144 MET cc_start: 0.5050 (mtp) cc_final: 0.3148 (tmm) REVERT: C 151 MET cc_start: 0.6643 (mmm) cc_final: 0.6203 (tpt) REVERT: C 694 ILE cc_start: 0.7316 (mt) cc_final: 0.7116 (mt) REVERT: C 985 SER cc_start: 0.9187 (m) cc_final: 0.8817 (p) outliers start: 64 outliers final: 46 residues processed: 262 average time/residue: 0.1429 time to fit residues: 62.9147 Evaluate side-chains 234 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1059 THR Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 837 PHE Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 903 LYS Chi-restraints excluded: chain C residue 1032 MET Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1112 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 20.0000 chunk 296 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 144 optimal weight: 40.0000 chunk 241 optimal weight: 3.9990 chunk 268 optimal weight: 10.0000 chunk 159 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 247 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.142033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.119563 restraints weight = 105492.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.117658 restraints weight = 93814.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.118285 restraints weight = 79978.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.118483 restraints weight = 64748.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.118595 restraints weight = 61335.402| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26616 Z= 0.158 Angle : 0.668 12.154 36350 Z= 0.341 Chirality : 0.047 0.292 4264 Planarity : 0.004 0.055 4569 Dihedral : 5.758 36.635 3439 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 2.09 % Allowed : 12.84 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.14), residues: 3163 helix: -0.69 (0.20), residues: 645 sheet: -0.84 (0.20), residues: 657 loop : -2.38 (0.13), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 126 TYR 0.017 0.001 TYR C1049 PHE 0.028 0.002 PHE B 83 TRP 0.023 0.002 TRP A 868 HIS 0.005 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (26505) covalent geometry : angle 0.65444 / 0.34 (36062) SS BOND : bond 0.00406 / 0.23 ( 45) SS BOND : angle 1.43172 / 0.93 ( 90) hydrogen bonds : bond 0.03924 / 2.53 ( 819) hydrogen bonds : angle 6.23743 / 4.33 ( 2379) link_ALPHA1-3 : bond 0.00460 / 0.24 ( 1) link_ALPHA1-3 : angle 1.40708 / 0.79 ( 3) link_ALPHA1-6 : bond 0.00391 / 0.21 ( 1) link_ALPHA1-6 : angle 1.64946 / 0.91 ( 3) link_BETA1-4 : bond 0.00460 / 0.35 ( 30) link_BETA1-4 : angle 1.43002 / 0.96 ( 90) link_NAG-ASN : bond 0.00303 / 0.22 ( 34) link_NAG-ASN : angle 2.00718 / 1.37 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 193 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.7552 (mtm) cc_final: 0.6516 (pmm) REVERT: A 417 MET cc_start: 0.0029 (mtt) cc_final: -0.0444 (ttm) REVERT: A 800 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7381 (tp) REVERT: A 942 ASN cc_start: 0.8420 (p0) cc_final: 0.8144 (p0) REVERT: A 1120 TYR cc_start: 0.6698 (m-10) cc_final: 0.6095 (t80) REVERT: B 263 MET cc_start: 0.6917 (ttm) cc_final: 0.6470 (ttp) REVERT: B 417 MET cc_start: 0.5101 (mmt) cc_final: 0.4524 (mmm) REVERT: B 884 MET cc_start: 0.7747 (mmm) cc_final: 0.7075 (mmm) REVERT: B 1013 GLU cc_start: 0.4493 (mm-30) cc_final: 0.3745 (mm-30) REVERT: B 1032 MET cc_start: 0.6460 (ttt) cc_final: 0.6093 (ttt) REVERT: C 144 MET cc_start: 0.5152 (mtp) cc_final: 0.3317 (tmm) REVERT: C 151 MET cc_start: 0.6785 (mmm) cc_final: 0.6407 (tpt) REVERT: C 605 ASP cc_start: 0.8384 (m-30) cc_final: 0.7921 (t0) REVERT: C 985 SER cc_start: 0.9176 (m) cc_final: 0.8802 (p) outliers start: 58 outliers final: 50 residues processed: 240 average time/residue: 0.1460 time to fit residues: 58.9724 Evaluate side-chains 237 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 186 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1092 PHE Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 357 ASN Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 837 PHE Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 228 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 903 LYS Chi-restraints excluded: chain C residue 1032 MET Chi-restraints excluded: chain C residue 1063 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 232 optimal weight: 0.2980 chunk 165 optimal weight: 1.9990 chunk 75 optimal weight: 30.0000 chunk 21 optimal weight: 4.9990 chunk 112 optimal weight: 9.9990 chunk 308 optimal weight: 4.9990 chunk 114 optimal weight: 30.0000 chunk 69 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 280 optimal weight: 3.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 661 HIS B 357 ASN B 630 GLN ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 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 = 0.4423 r_free = 0.4423 target = 0.141415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.119216 restraints weight = 105274.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.116981 restraints weight = 100119.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.117330 restraints weight = 90807.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.117678 restraints weight = 73516.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.117971 restraints weight = 64866.234| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 26616 Z= 0.183 Angle : 0.686 12.503 36350 Z= 0.350 Chirality : 0.047 0.297 4264 Planarity : 0.004 0.055 4569 Dihedral : 5.790 36.241 3439 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 2.30 % Allowed : 12.91 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.14), residues: 3163 helix: -0.75 (0.20), residues: 651 sheet: -0.88 (0.20), residues: 654 loop : -2.37 (0.13), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 18 TYR 0.017 0.002 TYR C1049 PHE 0.029 0.002 PHE B 83 TRP 0.018 0.002 TRP A 868 HIS 0.007 0.001 HIS A 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 (26505) covalent geometry : angle 0.67163 / 0.35 (36062) SS BOND : bond 0.00388 / 0.25 ( 45) SS BOND : angle 1.46909 / 0.96 ( 90) hydrogen bonds : bond 0.04044 / 2.59 ( 819) hydrogen bonds : angle 6.30551 / 4.38 ( 2379) link_ALPHA1-3 : bond 0.00413 / 0.22 ( 1) link_ALPHA1-3 : angle 1.40927 / 0.79 ( 3) link_ALPHA1-6 : bond 0.00354 / 0.19 ( 1) link_ALPHA1-6 : angle 1.68107 / 0.93 ( 3) link_BETA1-4 : bond 0.00473 / 0.37 ( 30) link_BETA1-4 : angle 1.42635 / 0.97 ( 90) link_NAG-ASN : bond 0.00330 / 0.24 ( 34) link_NAG-ASN : angle 2.07693 / 1.42 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 186 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 MET cc_start: -0.0116 (mtt) cc_final: -0.0552 (ttm) REVERT: A 800 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7456 (tp) REVERT: A 942 ASN cc_start: 0.8384 (p0) cc_final: 0.8113 (p0) REVERT: A 1120 TYR cc_start: 0.6650 (m-10) cc_final: 0.6047 (t80) REVERT: B 263 MET cc_start: 0.6942 (ttm) cc_final: 0.6473 (ttp) REVERT: B 417 MET cc_start: 0.5094 (mmt) cc_final: 0.4506 (mmm) REVERT: B 884 MET cc_start: 0.7915 (mmm) cc_final: 0.7241 (mmm) REVERT: B 1013 GLU cc_start: 0.4484 (mm-30) cc_final: 0.3801 (mm-30) REVERT: B 1032 MET cc_start: 0.6623 (ttt) cc_final: 0.6283 (ttt) REVERT: C 144 MET cc_start: 0.4927 (mtp) cc_final: 0.3281 (tmm) REVERT: C 985 SER cc_start: 0.9216 (m) cc_final: 0.8866 (p) outliers start: 64 outliers final: 56 residues processed: 235 average time/residue: 0.1480 time to fit residues: 57.5223 Evaluate side-chains 237 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 661 HIS Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 837 PHE Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 903 LYS Chi-restraints excluded: chain C residue 1032 MET Chi-restraints excluded: chain C residue 1063 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 123 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 289 optimal weight: 0.7980 chunk 209 optimal weight: 0.0970 chunk 115 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 230 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 overall best weight: 2.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.141605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.120362 restraints weight = 104808.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.119235 restraints weight = 99380.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.119601 restraints weight = 82645.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.119953 restraints weight = 65336.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.120237 restraints weight = 58428.865| |-----------------------------------------------------------------------------| r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.4922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26616 Z= 0.172 Angle : 0.681 12.938 36350 Z= 0.347 Chirality : 0.047 0.297 4264 Planarity : 0.004 0.056 4569 Dihedral : 5.750 35.641 3439 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 2.16 % Allowed : 13.17 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.14), residues: 3163 helix: -0.69 (0.20), residues: 648 sheet: -0.91 (0.20), residues: 658 loop : -2.34 (0.13), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 126 TYR 0.027 0.002 TYR A 886 PHE 0.028 0.002 PHE B 83 TRP 0.012 0.001 TRP B 423 HIS 0.005 0.001 HIS C 661 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (26505) covalent geometry : angle 0.66737 / 0.34 (36062) SS BOND : bond 0.00363 / 0.23 ( 45) SS BOND : angle 1.37505 / 0.91 ( 90) hydrogen bonds : bond 0.03981 / 2.56 ( 819) hydrogen bonds : angle 6.26986 / 4.37 ( 2379) link_ALPHA1-3 : bond 0.00422 / 0.22 ( 1) link_ALPHA1-3 : angle 1.40719 / 0.78 ( 3) link_ALPHA1-6 : bond 0.00359 / 0.19 ( 1) link_ALPHA1-6 : angle 1.65468 / 0.91 ( 3) link_BETA1-4 : bond 0.00465 / 0.36 ( 30) link_BETA1-4 : angle 1.40628 / 0.95 ( 90) link_NAG-ASN : bond 0.00306 / 0.22 ( 34) link_NAG-ASN : angle 2.06940 / 1.41 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 191 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 417 MET cc_start: 0.0051 (mtt) cc_final: -0.0511 (ttm) REVERT: A 800 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7395 (tp) REVERT: A 942 ASN cc_start: 0.8430 (p0) cc_final: 0.8153 (p0) REVERT: A 1120 TYR cc_start: 0.6661 (m-10) cc_final: 0.6068 (t80) REVERT: B 263 MET cc_start: 0.6965 (ttm) cc_final: 0.6609 (ttp) REVERT: B 417 MET cc_start: 0.5142 (mmt) cc_final: 0.4571 (mmm) REVERT: B 801 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7807 (mp0) REVERT: B 884 MET cc_start: 0.7886 (mmm) cc_final: 0.7217 (mmm) REVERT: B 1013 GLU cc_start: 0.4462 (mm-30) cc_final: 0.3783 (mm-30) REVERT: B 1032 MET cc_start: 0.6539 (ttt) cc_final: 0.6207 (ttt) REVERT: C 144 MET cc_start: 0.5323 (mtp) cc_final: 0.3403 (tmm) REVERT: C 151 MET cc_start: 0.5464 (tpt) cc_final: 0.5172 (tpt) REVERT: C 985 SER cc_start: 0.9196 (m) cc_final: 0.8788 (p) outliers start: 60 outliers final: 57 residues processed: 235 average time/residue: 0.1466 time to fit residues: 58.1519 Evaluate side-chains 244 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 186 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 152 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain A residue 800 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 988 THR Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1023 ASP Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 283 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 303 SER Chi-restraints excluded: chain B residue 606 VAL Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 674 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 837 PHE Chi-restraints excluded: chain B residue 850 ASP Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 975 ILE Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1071 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 88 TYR Chi-restraints excluded: chain C residue 138 PHE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 601 VAL Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 720 CYS Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 787 ILE Chi-restraints excluded: chain C residue 808 VAL Chi-restraints excluded: chain C residue 832 ILE Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 903 LYS Chi-restraints excluded: chain C residue 1032 MET Chi-restraints excluded: chain C residue 1063 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 7 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 chunk 219 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 186 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 236 optimal weight: 0.8980 chunk 290 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 227 optimal weight: 0.1980 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.141870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.120060 restraints weight = 104720.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.118323 restraints weight = 100236.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.118725 restraints weight = 85313.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.119187 restraints weight = 67953.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.119293 restraints weight = 60815.194| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26616 Z= 0.158 Angle : 0.665 12.855 36350 Z= 0.338 Chirality : 0.046 0.291 4264 Planarity : 0.004 0.056 4569 Dihedral : 5.630 33.548 3439 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 2.34 % Allowed : 13.13 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.14), residues: 3163 helix: -0.51 (0.21), residues: 635 sheet: -0.88 (0.20), residues: 637 loop : -2.32 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 126 TYR 0.018 0.001 TYR B1049 PHE 0.027 0.002 PHE B 83 TRP 0.014 0.001 TRP B 423 HIS 0.006 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (26505) covalent geometry : angle 0.65168 / 0.34 (36062) SS BOND : bond 0.00333 / 0.21 ( 45) SS BOND : angle 1.29937 / 0.86 ( 90) hydrogen bonds : bond 0.03863 / 2.49 ( 819) hydrogen bonds : angle 6.18446 / 4.32 ( 2379) link_ALPHA1-3 : bond 0.00402 / 0.21 ( 1) link_ALPHA1-3 : angle 1.38006 / 0.77 ( 3) link_ALPHA1-6 : bond 0.00360 / 0.19 ( 1) link_ALPHA1-6 : angle 1.61509 / 0.89 ( 3) link_BETA1-4 : bond 0.00452 / 0.35 ( 30) link_BETA1-4 : angle 1.38654 / 0.94 ( 90) link_NAG-ASN : bond 0.00270 / 0.20 ( 34) link_NAG-ASN : angle 1.99650 / 1.36 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4104.11 seconds wall clock time: 72 minutes 6.53 seconds (4326.53 seconds total)