Starting phenix.real_space_refine on Fri Sep 19 13:40:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6crz_7577/09_2025/6crz_7577.cif Found real_map, /net/cci-nas-00/data/ceres_data/6crz_7577/09_2025/6crz_7577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6crz_7577/09_2025/6crz_7577.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6crz_7577/09_2025/6crz_7577.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6crz_7577/09_2025/6crz_7577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6crz_7577/09_2025/6crz_7577.map" } resolution = 3.3 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= 0.008 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-2.0-5805/lib/python3.9/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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 12 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 dihedrals: 15 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 dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.37, per 1000 atoms: 0.21 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: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.24 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: 5.44 Time building geometry restraints manager: 2.89 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 - 21.97: 16032 21.97 - 43.94: 397 43.94 - 65.91: 57 65.91 - 87.88: 73 87.88 - 109.85: 45 Dihedral angle restraints: 16604 sinusoidal: 7270 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 16601 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 22.320 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1721 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 : 13.451 109.847 10465 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 aren 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 covalent geometry : bond 0.00701 (26505) covalent geometry : angle 1.00924 (36062) SS BOND : bond 0.00691 ( 45) SS BOND : angle 2.26278 ( 90) hydrogen bonds : bond 0.29573 ( 819) hydrogen bonds : angle 11.26271 ( 2379) link_ALPHA1-3 : bond 0.00620 ( 1) link_ALPHA1-3 : angle 1.30858 ( 3) link_ALPHA1-6 : bond 0.00151 ( 1) link_ALPHA1-6 : angle 1.66526 ( 3) link_BETA1-4 : bond 0.00866 ( 30) link_BETA1-4 : angle 2.70996 ( 90) link_NAG-ASN : bond 0.00602 ( 34) link_NAG-ASN : angle 3.59708 ( 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 365 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 0.899 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 96 ASN cc_start: 0.5115 (m-40) cc_final: 0.4296 (t0) REVERT: A 216 LEU cc_start: 0.2307 (mp) cc_final: 0.1712 (mt) REVERT: A 554 ASP cc_start: 0.4168 (t0) cc_final: 0.2825 (p0) REVERT: A 1084 TRP cc_start: 0.1030 (m100) cc_final: 0.0612 (m-90) REVERT: B 103 PHE cc_start: 0.5441 (m-10) cc_final: 0.5149 (m-10) REVERT: B 126 ARG cc_start: 0.3813 (mtp180) cc_final: 0.2417 (ttm170) REVERT: B 195 TYR cc_start: 0.3889 (m-10) cc_final: 0.2610 (m-10) REVERT: B 231 PHE cc_start: 0.5696 (p90) cc_final: 0.5490 (p90) REVERT: B 417 MET cc_start: 0.6001 (ttt) cc_final: 0.5459 (tmm) REVERT: B 783 ASN cc_start: 0.3708 (t0) cc_final: 0.3326 (p0) REVERT: C 254 VAL cc_start: 0.6414 (t) cc_final: 0.5317 (m) REVERT: C 417 MET cc_start: 0.2718 (tpp) cc_final: 0.0930 (ttt) REVERT: C 987 GLN cc_start: 0.3659 (tp40) cc_final: 0.3447 (tt0) REVERT: C 1006 LEU cc_start: 0.5971 (tp) cc_final: 0.4955 (mp) REVERT: C 1095 GLN cc_start: 0.0098 (mm-40) cc_final: -0.0280 (mt0) outliers start: 1 outliers final: 0 residues processed: 365 average time/residue: 0.1591 time to fit residues: 94.0312 Evaluate side-chains 217 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0170 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN A 611 HIS A 661 HIS A 883 GLN ** A 908 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1117 ASN B 118 ASN B 641 HIS B 733 ASN B 766 GLN B 786 GLN B 908 GLN B1065 HIS ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 347 ASN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 889 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5242 r_free = 0.5242 target = 0.292327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.5148 r_free = 0.5148 target = 0.280832 restraints weight = 54443.430| |-----------------------------------------------------------------------------| r_work (start): 0.5144 rms_B_bonded: 2.11 r_work: 0.5030 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.5030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2162 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 26616 Z= 0.162 Angle : 0.735 8.714 36350 Z= 0.377 Chirality : 0.048 0.261 4264 Planarity : 0.005 0.076 4569 Dihedral : 10.508 71.976 4798 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.22 % Allowed : 4.89 % Favored : 93.88 % 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 aren not related in a simple way. whole: -3.12 (0.13), residues: 3163 helix: -2.31 (0.17), residues: 636 sheet: -1.14 (0.19), residues: 634 loop : -2.41 (0.12), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 126 TYR 0.030 0.002 TYR C 252 PHE 0.024 0.002 PHE C 83 TRP 0.020 0.001 TRP B 423 HIS 0.005 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00346 (26505) covalent geometry : angle 0.71121 (36062) SS BOND : bond 0.00734 ( 45) SS BOND : angle 1.79333 ( 90) hydrogen bonds : bond 0.05047 ( 819) hydrogen bonds : angle 7.07064 ( 2379) link_ALPHA1-3 : bond 0.01033 ( 1) link_ALPHA1-3 : angle 3.87045 ( 3) link_ALPHA1-6 : bond 0.01267 ( 1) link_ALPHA1-6 : angle 1.15507 ( 3) link_BETA1-4 : bond 0.00546 ( 30) link_BETA1-4 : angle 2.47474 ( 90) link_NAG-ASN : bond 0.00499 ( 34) link_NAG-ASN : angle 2.25492 ( 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 285 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 251 time to evaluate : 0.750 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 189 ASN cc_start: 0.4301 (p0) cc_final: 0.3536 (t0) REVERT: A 216 LEU cc_start: 0.2824 (mp) cc_final: 0.2604 (pp) REVERT: A 263 MET cc_start: -0.0973 (tmm) cc_final: -0.2933 (ttp) REVERT: A 341 GLU cc_start: 0.4188 (tp30) cc_final: 0.3970 (tp30) REVERT: B 195 TYR cc_start: 0.3642 (m-10) cc_final: 0.2402 (m-10) REVERT: B 213 PHE cc_start: 0.2400 (t80) cc_final: 0.2015 (p90) REVERT: B 417 MET cc_start: 0.4947 (ttt) cc_final: 0.4518 (tmm) REVERT: B 746 ASN cc_start: 0.1770 (m-40) cc_final: 0.1549 (m-40) REVERT: B 869 THR cc_start: 0.3710 (p) cc_final: 0.2962 (p) REVERT: B 891 ILE cc_start: 0.2204 (pt) cc_final: -0.0034 (mp) REVERT: B 1011 MET cc_start: 0.3599 (tpt) cc_final: 0.3002 (tpt) REVERT: C 804 LEU cc_start: 0.4955 (OUTLIER) cc_final: 0.4314 (tp) REVERT: C 1066 GLU cc_start: 0.1875 (mt-10) cc_final: 0.1055 (tt0) outliers start: 34 outliers final: 19 residues processed: 275 average time/residue: 0.1478 time to fit residues: 68.6774 Evaluate side-chains 216 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 687 ILE Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 943 THR Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 808 VAL Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 230 ASN Chi-restraints excluded: chain C residue 804 LEU Chi-restraints excluded: chain C residue 822 CYS Chi-restraints excluded: chain C residue 833 CYS Chi-restraints excluded: chain C residue 919 SER Chi-restraints excluded: chain C residue 925 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 154 optimal weight: 7.9990 chunk 206 optimal weight: 0.6980 chunk 33 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 253 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 40.0000 chunk 300 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 ASN A 937 ASN A 984 GLN B 122 ASN B 155 ASN B 661 HIS B 756 GLN B 908 GLN B 936 GLN B 984 GLN C 201 GLN C 347 ASN C 626 ASN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 984 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5243 r_free = 0.5243 target = 0.293343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.5154 r_free = 0.5154 target = 0.281817 restraints weight = 53678.800| |-----------------------------------------------------------------------------| r_work (start): 0.5133 rms_B_bonded: 1.79 r_work: 0.5004 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.5004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2883 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 26616 Z= 0.161 Angle : 0.714 13.880 36350 Z= 0.358 Chirality : 0.048 0.311 4264 Planarity : 0.005 0.080 4569 Dihedral : 7.762 54.313 4798 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.19 % Allowed : 6.58 % Favored : 92.23 % 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 aren not related in a simple way. whole: -2.51 (0.13), residues: 3163 helix: -1.21 (0.19), residues: 616 sheet: -0.69 (0.20), residues: 604 loop : -2.24 (0.12), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 38 TYR 0.021 0.002 TYR A 689 PHE 0.029 0.002 PHE B 578 TRP 0.040 0.002 TRP C 619 HIS 0.007 0.001 HIS B 641 Details of bonding type rmsd covalent geometry : bond 0.00345 (26505) covalent geometry : angle 0.68353 (36062) SS BOND : bond 0.00420 ( 45) SS BOND : angle 1.59601 ( 90) hydrogen bonds : bond 0.04959 ( 819) hydrogen bonds : angle 6.41597 ( 2379) link_ALPHA1-3 : bond 0.01664 ( 1) link_ALPHA1-3 : angle 1.63819 ( 3) link_ALPHA1-6 : bond 0.00899 ( 1) link_ALPHA1-6 : angle 1.33692 ( 3) link_BETA1-4 : bond 0.00668 ( 30) link_BETA1-4 : angle 2.28748 ( 90) link_NAG-ASN : bond 0.00548 ( 34) link_NAG-ASN : angle 3.06510 ( 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 278 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.3023 (mtm-85) cc_final: 0.1776 (mtt90) REVERT: A 51 THR cc_start: 0.3235 (OUTLIER) cc_final: 0.2839 (m) REVERT: A 72 ILE cc_start: 0.0067 (tt) cc_final: -0.0149 (tt) REVERT: A 216 LEU cc_start: 0.3331 (mp) cc_final: 0.3005 (pp) REVERT: A 1084 TRP cc_start: 0.1586 (m100) cc_final: -0.0227 (p90) REVERT: B 195 TYR cc_start: 0.3814 (m-10) cc_final: 0.2906 (m-10) REVERT: B 231 PHE cc_start: 0.4920 (p90) cc_final: 0.4324 (p90) REVERT: B 417 MET cc_start: 0.5304 (ttt) cc_final: 0.4257 (tmm) REVERT: B 715 LYS cc_start: 0.5073 (ptpt) cc_final: 0.4038 (mtpt) REVERT: B 752 ILE cc_start: 0.6743 (mt) cc_final: 0.6343 (mt) REVERT: C 417 MET cc_start: 0.2246 (tpp) cc_final: 0.1289 (ptt) REVERT: C 529 PHE cc_start: 0.1400 (m-80) cc_final: 0.0644 (m-80) outliers start: 33 outliers final: 21 residues processed: 268 average time/residue: 0.1531 time to fit residues: 68.7031 Evaluate side-chains 222 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 819 TYR Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 856 THR Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 822 CYS Chi-restraints excluded: chain C residue 833 CYS Chi-restraints excluded: chain C residue 925 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 155 optimal weight: 5.9990 chunk 114 optimal weight: 0.0970 chunk 107 optimal weight: 0.0270 chunk 306 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 204 optimal weight: 0.6980 chunk 301 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 221 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1090 ASN B 118 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 835 GLN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 883 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5208 r_free = 0.5208 target = 0.287589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.5079 r_free = 0.5079 target = 0.271378 restraints weight = 50875.581| |-----------------------------------------------------------------------------| r_work (start): 0.5073 rms_B_bonded: 1.90 r_work: 0.4981 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.4981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3568 moved from start: 0.5440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 26616 Z= 0.174 Angle : 0.709 16.743 36350 Z= 0.365 Chirality : 0.048 0.374 4264 Planarity : 0.005 0.063 4569 Dihedral : 6.664 59.857 4798 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.40 % Rotamer: Outliers : 1.65 % Allowed : 8.06 % Favored : 90.29 % 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 aren not related in a simple way. whole: -2.34 (0.14), residues: 3163 helix: -0.89 (0.19), residues: 641 sheet: -0.72 (0.20), residues: 635 loop : -2.18 (0.13), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 183 TYR 0.021 0.002 TYR A 689 PHE 0.036 0.002 PHE B 157 TRP 0.012 0.001 TRP B 423 HIS 0.008 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00378 (26505) covalent geometry : angle 0.68279 (36062) SS BOND : bond 0.01079 ( 45) SS BOND : angle 1.66104 ( 90) hydrogen bonds : bond 0.04644 ( 819) hydrogen bonds : angle 6.18778 ( 2379) link_ALPHA1-3 : bond 0.00707 ( 1) link_ALPHA1-3 : angle 2.91303 ( 3) link_ALPHA1-6 : bond 0.01210 ( 1) link_ALPHA1-6 : angle 0.89322 ( 3) link_BETA1-4 : bond 0.00545 ( 30) link_BETA1-4 : angle 1.73219 ( 90) link_NAG-ASN : bond 0.01449 ( 34) link_NAG-ASN : angle 2.97647 ( 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 276 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 0.931 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 51 THR cc_start: 0.3825 (OUTLIER) cc_final: 0.3469 (m) REVERT: A 263 MET cc_start: -0.0087 (tmm) cc_final: -0.1370 (mtp) REVERT: A 705 THR cc_start: 0.3047 (OUTLIER) cc_final: 0.2334 (m) REVERT: B 155 ASN cc_start: 0.1003 (OUTLIER) cc_final: 0.0711 (p0) REVERT: B 195 TYR cc_start: 0.3720 (m-10) cc_final: 0.2802 (m-10) REVERT: B 231 PHE cc_start: 0.4723 (p90) cc_final: 0.4458 (p90) REVERT: B 263 MET cc_start: 0.0614 (mmm) cc_final: -0.0413 (tpt) REVERT: B 417 MET cc_start: 0.4725 (ttt) cc_final: 0.4044 (tmm) REVERT: B 605 ASP cc_start: 0.3433 (OUTLIER) cc_final: 0.2887 (m-30) REVERT: B 849 ASP cc_start: 0.6533 (t0) cc_final: 0.6249 (t0) REVERT: B 882 MET cc_start: 0.2412 (mmp) cc_final: 0.1756 (mmp) REVERT: B 920 LEU cc_start: 0.7641 (mt) cc_final: 0.7385 (mt) REVERT: B 1011 MET cc_start: 0.8246 (tpp) cc_final: 0.7958 (tpt) REVERT: C 417 MET cc_start: 0.2057 (tpp) cc_final: 0.1391 (ptt) REVERT: C 619 TRP cc_start: 0.3572 (m-90) cc_final: 0.3239 (m-90) REVERT: C 709 MET cc_start: 0.6570 (ppp) cc_final: 0.6129 (ptp) REVERT: C 722 MET cc_start: 0.2762 (mtm) cc_final: 0.2085 (mtm) REVERT: C 724 ILE cc_start: 0.0547 (OUTLIER) cc_final: -0.0168 (pt) outliers start: 46 outliers final: 28 residues processed: 265 average time/residue: 0.1624 time to fit residues: 69.6670 Evaluate side-chains 223 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 705 THR Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 819 TYR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1033 SER Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 118 ASN Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 637 ILE Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 744 GLN Chi-restraints excluded: chain C residue 822 CYS Chi-restraints excluded: chain C residue 833 CYS Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1043 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 198 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 162 optimal weight: 2.9990 chunk 136 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 308 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 280 GLN A 766 GLN A 935 ASN A1065 HIS ** A1090 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 ASN B 280 GLN B 896 ASN B 951 ASN ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 818 GLN C1018 GLN C1030 HIS ** C1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5126 r_free = 0.5126 target = 0.277587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4949 r_free = 0.4949 target = 0.255735 restraints weight = 49112.122| |-----------------------------------------------------------------------------| r_work (start): 0.4931 rms_B_bonded: 2.30 r_work: 0.4719 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5056 moved from start: 0.8149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.227 26616 Z= 0.272 Angle : 0.901 25.890 36350 Z= 0.471 Chirality : 0.053 0.537 4264 Planarity : 0.007 0.114 4569 Dihedral : 7.031 49.781 4798 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.30 % Allowed : 9.06 % Favored : 88.63 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: -2.51 (0.13), residues: 3163 helix: -1.28 (0.19), residues: 628 sheet: -0.80 (0.22), residues: 554 loop : -2.16 (0.12), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 563 TYR 0.036 0.002 TYR B1029 PHE 0.057 0.003 PHE B 185 TRP 0.011 0.002 TRP C 868 HIS 0.012 0.002 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00621 (26505) covalent geometry : angle 0.87372 (36062) SS BOND : bond 0.01256 ( 45) SS BOND : angle 1.96303 ( 90) hydrogen bonds : bond 0.06230 ( 819) hydrogen bonds : angle 6.97908 ( 2379) link_ALPHA1-3 : bond 0.00434 ( 1) link_ALPHA1-3 : angle 1.92763 ( 3) link_ALPHA1-6 : bond 0.01725 ( 1) link_ALPHA1-6 : angle 1.16254 ( 3) link_BETA1-4 : bond 0.00620 ( 30) link_BETA1-4 : angle 1.83433 ( 90) link_NAG-ASN : bond 0.00904 ( 34) link_NAG-ASN : angle 3.62819 ( 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 326 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 262 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 THR cc_start: 0.4025 (OUTLIER) cc_final: 0.3758 (m) REVERT: B 195 TYR cc_start: 0.4395 (m-10) cc_final: 0.3520 (m-10) REVERT: B 219 ILE cc_start: 0.4921 (mm) cc_final: 0.4708 (mm) REVERT: B 231 PHE cc_start: 0.5572 (p90) cc_final: 0.5181 (p90) REVERT: B 263 MET cc_start: 0.2247 (mmm) cc_final: 0.1801 (mmm) REVERT: B 417 MET cc_start: 0.4961 (ttt) cc_final: 0.4119 (tmm) REVERT: B 605 ASP cc_start: 0.4032 (OUTLIER) cc_final: 0.3723 (m-30) REVERT: B 660 TYR cc_start: 0.4320 (OUTLIER) cc_final: 0.3218 (t80) REVERT: B 932 ASP cc_start: 0.7208 (t0) cc_final: 0.6883 (t0) REVERT: B 946 LYS cc_start: 0.6975 (mmtt) cc_final: 0.6378 (tttt) REVERT: B 1013 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: C 151 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.6031 (mpp) REVERT: C 195 TYR cc_start: 0.4299 (m-10) cc_final: 0.3940 (m-10) REVERT: C 263 MET cc_start: 0.2194 (ptp) cc_final: 0.1848 (mmm) REVERT: C 405 ILE cc_start: 0.5355 (OUTLIER) cc_final: 0.5058 (pt) REVERT: C 417 MET cc_start: 0.2624 (tpp) cc_final: 0.1563 (ptt) REVERT: C 702 ILE cc_start: -0.0667 (OUTLIER) cc_final: -0.1665 (pt) REVERT: C 722 MET cc_start: 0.3303 (mtm) cc_final: 0.2602 (mtm) REVERT: C 724 ILE cc_start: 0.2259 (OUTLIER) cc_final: 0.1475 (pt) outliers start: 64 outliers final: 31 residues processed: 313 average time/residue: 0.1645 time to fit residues: 82.4925 Evaluate side-chains 232 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 312 ASP Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 819 TYR Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 991 THR Chi-restraints excluded: chain A residue 1032 MET Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 923 THR Chi-restraints excluded: chain B residue 1013 GLU Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 702 ILE Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 724 ILE Chi-restraints excluded: chain C residue 818 GLN Chi-restraints excluded: chain C residue 822 CYS Chi-restraints excluded: chain C residue 833 CYS Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1011 MET Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 42 optimal weight: 0.8980 chunk 293 optimal weight: 0.0060 chunk 35 optimal weight: 0.0270 chunk 56 optimal weight: 0.7980 chunk 234 optimal weight: 5.9990 chunk 128 optimal weight: 0.0470 chunk 317 optimal weight: 0.8980 chunk 119 optimal weight: 10.0000 chunk 278 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 overall best weight: 0.3152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 599 GLN A 910 ASN A 937 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 896 ASN ** B 984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 626 ASN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 632 GLN C 818 GLN C1018 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5134 r_free = 0.5134 target = 0.278947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.259316 restraints weight = 50606.786| |-----------------------------------------------------------------------------| r_work (start): 0.4960 rms_B_bonded: 2.11 r_work: 0.4753 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4956 moved from start: 0.8397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26616 Z= 0.122 Angle : 0.624 17.969 36350 Z= 0.319 Chirality : 0.045 0.201 4264 Planarity : 0.004 0.058 4569 Dihedral : 6.090 46.661 4798 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.26 % Allowed : 10.94 % Favored : 87.81 % 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 aren not related in a simple way. whole: -2.08 (0.14), residues: 3163 helix: -0.49 (0.20), residues: 643 sheet: -0.71 (0.21), residues: 600 loop : -2.00 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 99 TYR 0.031 0.001 TYR A 689 PHE 0.027 0.002 PHE B 629 TRP 0.010 0.001 TRP A 868 HIS 0.009 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00259 (26505) covalent geometry : angle 0.59668 (36062) SS BOND : bond 0.00377 ( 45) SS BOND : angle 1.44921 ( 90) hydrogen bonds : bond 0.04224 ( 819) hydrogen bonds : angle 6.04878 ( 2379) link_ALPHA1-3 : bond 0.00571 ( 1) link_ALPHA1-3 : angle 1.69604 ( 3) link_ALPHA1-6 : bond 0.00920 ( 1) link_ALPHA1-6 : angle 1.15822 ( 3) link_BETA1-4 : bond 0.00512 ( 30) link_BETA1-4 : angle 1.59291 ( 90) link_NAG-ASN : bond 0.00525 ( 34) link_NAG-ASN : angle 2.91534 ( 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 246 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 738 TYR cc_start: 0.2171 (m-80) cc_final: 0.1880 (m-80) REVERT: A 1084 TRP cc_start: 0.1811 (m100) cc_final: -0.0466 (p90) REVERT: B 37 MET cc_start: 0.3055 (tpp) cc_final: 0.2243 (tpt) REVERT: B 195 TYR cc_start: 0.4149 (m-10) cc_final: 0.3227 (m-10) REVERT: B 219 ILE cc_start: 0.4429 (mm) cc_final: 0.4062 (mm) REVERT: B 231 PHE cc_start: 0.5334 (p90) cc_final: 0.4811 (p90) REVERT: B 417 MET cc_start: 0.4757 (ttt) cc_final: 0.3953 (tmm) REVERT: B 637 ILE cc_start: 0.3444 (mt) cc_final: 0.3166 (mt) REVERT: B 932 ASP cc_start: 0.6964 (t0) cc_final: 0.6717 (t0) REVERT: C 37 MET cc_start: 0.3345 (mmm) cc_final: 0.2299 (tpp) REVERT: C 417 MET cc_start: 0.2285 (tpp) cc_final: 0.1423 (ptt) REVERT: C 722 MET cc_start: 0.3071 (mtm) cc_final: 0.2312 (mtm) outliers start: 35 outliers final: 20 residues processed: 239 average time/residue: 0.1513 time to fit residues: 60.1312 Evaluate side-chains 197 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 650 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 819 TYR Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 961 ASP Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 822 CYS Chi-restraints excluded: chain C residue 1071 PHE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 63 optimal weight: 0.8980 chunk 270 optimal weight: 0.7980 chunk 41 optimal weight: 30.0000 chunk 95 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 271 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 77 optimal weight: 0.0030 chunk 258 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 GLN A 936 GLN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN C 630 GLN C 889 ASN C 984 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5120 r_free = 0.5120 target = 0.276959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4948 r_free = 0.4948 target = 0.256312 restraints weight = 49933.831| |-----------------------------------------------------------------------------| r_work (start): 0.4933 rms_B_bonded: 1.98 r_work: 0.4724 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.4724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5093 moved from start: 0.8868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26616 Z= 0.123 Angle : 0.618 17.755 36350 Z= 0.317 Chirality : 0.044 0.240 4264 Planarity : 0.004 0.049 4569 Dihedral : 5.832 53.169 4798 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.19 % Allowed : 11.65 % Favored : 87.16 % 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 aren not related in a simple way. whole: -1.84 (0.14), residues: 3163 helix: -0.14 (0.20), residues: 640 sheet: -0.56 (0.21), residues: 643 loop : -1.94 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 232 TYR 0.021 0.001 TYR B 771 PHE 0.025 0.002 PHE B 629 TRP 0.011 0.001 TRP B 423 HIS 0.009 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00269 (26505) covalent geometry : angle 0.58949 (36062) SS BOND : bond 0.00420 ( 45) SS BOND : angle 1.58183 ( 90) hydrogen bonds : bond 0.04107 ( 819) hydrogen bonds : angle 5.78574 ( 2379) link_ALPHA1-3 : bond 0.00680 ( 1) link_ALPHA1-3 : angle 1.41497 ( 3) link_ALPHA1-6 : bond 0.00807 ( 1) link_ALPHA1-6 : angle 1.24466 ( 3) link_BETA1-4 : bond 0.00496 ( 30) link_BETA1-4 : angle 1.56441 ( 90) link_NAG-ASN : bond 0.00551 ( 34) link_NAG-ASN : angle 2.98296 ( 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 222 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.4133 (mtm-85) cc_final: 0.3867 (mtm110) REVERT: A 738 TYR cc_start: 0.2397 (m-80) cc_final: 0.2174 (m-80) REVERT: A 882 MET cc_start: 0.1551 (tpt) cc_final: 0.1097 (ttm) REVERT: A 1084 TRP cc_start: 0.2013 (m100) cc_final: -0.0351 (p90) REVERT: B 37 MET cc_start: 0.3392 (tpp) cc_final: 0.2642 (tpt) REVERT: B 195 TYR cc_start: 0.4314 (m-10) cc_final: 0.3360 (m-10) REVERT: B 219 ILE cc_start: 0.4688 (mm) cc_final: 0.4002 (mm) REVERT: B 231 PHE cc_start: 0.5573 (p90) cc_final: 0.5006 (p90) REVERT: B 417 MET cc_start: 0.4874 (ttt) cc_final: 0.3860 (tmm) REVERT: B 769 GLN cc_start: 0.4902 (tp-100) cc_final: 0.4571 (tp-100) REVERT: B 932 ASP cc_start: 0.7042 (t0) cc_final: 0.6826 (t0) REVERT: C 37 MET cc_start: 0.3683 (mmm) cc_final: 0.2411 (tpp) REVERT: C 405 ILE cc_start: 0.5408 (OUTLIER) cc_final: 0.5199 (pt) REVERT: C 417 MET cc_start: 0.2286 (tpp) cc_final: 0.1358 (ptm) REVERT: C 722 MET cc_start: 0.3354 (mtm) cc_final: 0.2482 (mtm) outliers start: 33 outliers final: 25 residues processed: 216 average time/residue: 0.1518 time to fit residues: 55.1582 Evaluate side-chains 193 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain A residue 819 TYR Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 773 THR Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 895 GLN Chi-restraints excluded: chain B residue 985 SER Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 822 CYS Chi-restraints excluded: chain C residue 833 CYS Chi-restraints excluded: chain C residue 878 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 9.9990 chunk 296 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 264 optimal weight: 9.9990 chunk 94 optimal weight: 2.9990 chunk 144 optimal weight: 7.9990 chunk 241 optimal weight: 1.9990 chunk 268 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 247 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 721 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN B 883 GLN ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 818 GLN C 877 GLN C1030 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5013 r_free = 0.5013 target = 0.264584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.239770 restraints weight = 48117.094| |-----------------------------------------------------------------------------| r_work (start): 0.4778 rms_B_bonded: 2.55 r_work: 0.4472 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5886 moved from start: 1.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 26616 Z= 0.230 Angle : 0.839 20.314 36350 Z= 0.428 Chirality : 0.052 0.803 4264 Planarity : 0.006 0.128 4569 Dihedral : 6.639 59.701 4798 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.73 % Allowed : 11.73 % Favored : 86.55 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: -2.19 (0.14), residues: 3163 helix: -0.67 (0.19), residues: 639 sheet: -0.52 (0.22), residues: 563 loop : -2.11 (0.12), residues: 1961 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 996 TYR 0.049 0.002 TYR A 195 PHE 0.047 0.003 PHE A1057 TRP 0.014 0.002 TRP B 868 HIS 0.013 0.002 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00527 (26505) covalent geometry : angle 0.80633 (36062) SS BOND : bond 0.00506 ( 45) SS BOND : angle 2.00898 ( 90) hydrogen bonds : bond 0.05733 ( 819) hydrogen bonds : angle 6.62809 ( 2379) link_ALPHA1-3 : bond 0.00518 ( 1) link_ALPHA1-3 : angle 1.44038 ( 3) link_ALPHA1-6 : bond 0.00706 ( 1) link_ALPHA1-6 : angle 1.31854 ( 3) link_BETA1-4 : bond 0.00566 ( 30) link_BETA1-4 : angle 1.71076 ( 90) link_NAG-ASN : bond 0.01484 ( 34) link_NAG-ASN : angle 3.81166 ( 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 282 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 621 ILE cc_start: 0.6474 (mp) cc_final: 0.6218 (pt) REVERT: A 679 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7998 (ptm) REVERT: A 770 MET cc_start: 0.5329 (tpt) cc_final: 0.4360 (ptm) REVERT: B 37 MET cc_start: 0.3200 (tpp) cc_final: 0.2959 (tpt) REVERT: B 195 TYR cc_start: 0.4970 (m-10) cc_final: 0.3944 (m-10) REVERT: B 219 ILE cc_start: 0.5840 (mm) cc_final: 0.5559 (mm) REVERT: B 231 PHE cc_start: 0.5924 (p90) cc_final: 0.5234 (p90) REVERT: B 417 MET cc_start: 0.4487 (ttt) cc_final: 0.3691 (tmm) REVERT: B 592 SER cc_start: 0.8033 (OUTLIER) cc_final: 0.7832 (m) REVERT: B 660 TYR cc_start: 0.6567 (OUTLIER) cc_final: 0.6266 (t80) REVERT: B 766 GLN cc_start: 0.7699 (pt0) cc_final: 0.7411 (pt0) REVERT: B 770 MET cc_start: 0.7397 (tpt) cc_final: 0.7149 (tpt) REVERT: B 771 TYR cc_start: 0.5574 (m-80) cc_final: 0.4949 (m-10) REVERT: B 939 GLN cc_start: 0.8090 (mm-40) cc_final: 0.7803 (mm110) REVERT: C 101 TRP cc_start: 0.6190 (m-90) cc_final: 0.5765 (m-90) REVERT: C 125 ILE cc_start: 0.7797 (mp) cc_final: 0.7457 (mt) REVERT: C 405 ILE cc_start: 0.5254 (OUTLIER) cc_final: 0.5043 (pt) REVERT: C 417 MET cc_start: 0.2454 (tpp) cc_final: 0.1621 (tpp) REVERT: C 539 THR cc_start: 0.4206 (p) cc_final: 0.3938 (t) REVERT: C 722 MET cc_start: 0.4282 (mtm) cc_final: 0.3610 (mtm) REVERT: C 784 PHE cc_start: 0.7295 (m-10) cc_final: 0.7059 (m-10) REVERT: C 899 TYR cc_start: 0.3299 (m-80) cc_final: 0.3051 (m-80) REVERT: C 952 PHE cc_start: 0.4445 (t80) cc_final: 0.4047 (t80) outliers start: 48 outliers final: 30 residues processed: 269 average time/residue: 0.1688 time to fit residues: 74.4390 Evaluate side-chains 209 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 647 GLU Chi-restraints excluded: chain A residue 679 MET Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 592 SER Chi-restraints excluded: chain B residue 637 ILE Chi-restraints excluded: chain B residue 660 TYR Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 786 GLN Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 527 PHE Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 822 CYS Chi-restraints excluded: chain C residue 833 CYS Chi-restraints excluded: chain C residue 1000 ILE Chi-restraints excluded: chain C residue 1023 ASP Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 232 optimal weight: 0.6980 chunk 165 optimal weight: 0.7980 chunk 75 optimal weight: 0.0370 chunk 21 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 308 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 123 optimal weight: 7.9990 chunk 280 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 HIS B 786 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 818 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5033 r_free = 0.5033 target = 0.266627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.243247 restraints weight = 48122.835| |-----------------------------------------------------------------------------| r_work (start): 0.4809 rms_B_bonded: 2.54 r_work: 0.4509 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 1.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 26616 Z= 0.138 Angle : 0.688 17.526 36350 Z= 0.346 Chirality : 0.046 0.278 4264 Planarity : 0.005 0.079 4569 Dihedral : 7.642 113.708 4798 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.29 % Allowed : 13.17 % Favored : 85.54 % 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 aren not related in a simple way. whole: -2.00 (0.14), residues: 3163 helix: -0.27 (0.20), residues: 641 sheet: -0.82 (0.20), residues: 632 loop : -1.96 (0.13), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1089 TYR 0.019 0.001 TYR A 197 PHE 0.025 0.002 PHE C 527 TRP 0.015 0.001 TRP A1084 HIS 0.009 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00300 (26505) covalent geometry : angle 0.64993 (36062) SS BOND : bond 0.00340 ( 45) SS BOND : angle 1.72758 ( 90) hydrogen bonds : bond 0.04392 ( 819) hydrogen bonds : angle 6.02013 ( 2379) link_ALPHA1-3 : bond 0.00459 ( 1) link_ALPHA1-3 : angle 1.51129 ( 3) link_ALPHA1-6 : bond 0.00703 ( 1) link_ALPHA1-6 : angle 1.31702 ( 3) link_BETA1-4 : bond 0.00536 ( 30) link_BETA1-4 : angle 1.52714 ( 90) link_NAG-ASN : bond 0.01080 ( 34) link_NAG-ASN : angle 3.80156 ( 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 219 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.4967 (mtp180) cc_final: 0.4690 (mtm180) REVERT: A 529 PHE cc_start: 0.2446 (m-10) cc_final: 0.1559 (m-80) REVERT: A 621 ILE cc_start: 0.6614 (mp) cc_final: 0.6393 (pt) REVERT: A 770 MET cc_start: 0.5069 (tpt) cc_final: 0.3953 (ptm) REVERT: A 1084 TRP cc_start: 0.1752 (m100) cc_final: 0.0073 (p90) REVERT: B 195 TYR cc_start: 0.4361 (m-10) cc_final: 0.3526 (m-10) REVERT: B 417 MET cc_start: 0.4585 (ttt) cc_final: 0.3626 (tmm) REVERT: B 899 TYR cc_start: 0.7837 (m-80) cc_final: 0.6870 (m-80) REVERT: B 939 GLN cc_start: 0.8081 (mm-40) cc_final: 0.7815 (mm110) REVERT: C 125 ILE cc_start: 0.7768 (mp) cc_final: 0.7426 (mt) REVERT: C 187 PHE cc_start: 0.5489 (m-10) cc_final: 0.5090 (m-10) REVERT: C 417 MET cc_start: 0.2536 (tpp) cc_final: 0.1654 (tpp) REVERT: C 722 MET cc_start: 0.4072 (mtm) cc_final: 0.2602 (mtm) REVERT: C 899 TYR cc_start: 0.2954 (m-80) cc_final: 0.2681 (m-80) outliers start: 36 outliers final: 18 residues processed: 210 average time/residue: 0.1663 time to fit residues: 58.0120 Evaluate side-chains 180 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1047 VAL Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain B residue 262 PHE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain C residue 33 HIS Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 822 CYS Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 962 ILE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 123 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 289 optimal weight: 10.0000 chunk 209 optimal weight: 0.9980 chunk 115 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 230 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 ASN A 818 GLN ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 786 GLN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN B 936 GLN ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 984 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4965 r_free = 0.4965 target = 0.259036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.231240 restraints weight = 46769.879| |-----------------------------------------------------------------------------| r_work (start): 0.4697 rms_B_bonded: 2.94 r_work (final): 0.4697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5417 moved from start: 1.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 26616 Z= 0.197 Angle : 0.764 17.298 36350 Z= 0.392 Chirality : 0.049 0.283 4264 Planarity : 0.006 0.224 4569 Dihedral : 7.779 115.945 4798 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.83 % Allowed : 13.42 % Favored : 85.76 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: -2.12 (0.14), residues: 3163 helix: -0.29 (0.20), residues: 634 sheet: -0.85 (0.21), residues: 647 loop : -2.10 (0.13), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.034 0.001 ARG A 48 TYR 0.036 0.002 TYR A 53 PHE 0.028 0.002 PHE C 952 TRP 0.016 0.001 TRP C1084 HIS 0.061 0.002 HIS C 33 Details of bonding type rmsd covalent geometry : bond 0.00445 (26505) covalent geometry : angle 0.73282 (36062) SS BOND : bond 0.00499 ( 45) SS BOND : angle 1.90474 ( 90) hydrogen bonds : bond 0.05071 ( 819) hydrogen bonds : angle 6.32226 ( 2379) link_ALPHA1-3 : bond 0.00547 ( 1) link_ALPHA1-3 : angle 1.40209 ( 3) link_ALPHA1-6 : bond 0.00656 ( 1) link_ALPHA1-6 : angle 1.35573 ( 3) link_BETA1-4 : bond 0.00524 ( 30) link_BETA1-4 : angle 1.61853 ( 90) link_NAG-ASN : bond 0.00829 ( 34) link_NAG-ASN : angle 3.52429 ( 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 224 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 38 ARG cc_start: 0.5167 (mtp180) cc_final: 0.4628 (mtm110) REVERT: A 228 ILE cc_start: 0.6167 (mm) cc_final: 0.5924 (tp) REVERT: A 851 MET cc_start: 0.6639 (ttm) cc_final: 0.6402 (mtp) REVERT: B 195 TYR cc_start: 0.3577 (m-10) cc_final: 0.3015 (m-10) REVERT: B 306 ARG cc_start: 0.7110 (mmm-85) cc_final: 0.6829 (mmm-85) REVERT: B 417 MET cc_start: 0.4078 (ttt) cc_final: 0.3770 (tmm) REVERT: B 877 GLN cc_start: 0.6985 (tm-30) cc_final: 0.6575 (tm-30) REVERT: B 1112 ILE cc_start: 0.5722 (mm) cc_final: 0.5378 (mt) REVERT: C 101 TRP cc_start: 0.6090 (m-90) cc_final: 0.5710 (m-90) REVERT: C 125 ILE cc_start: 0.7525 (mp) cc_final: 0.7171 (mt) REVERT: C 187 PHE cc_start: 0.5469 (m-10) cc_final: 0.5151 (m-10) REVERT: C 417 MET cc_start: 0.2304 (tpp) cc_final: 0.1419 (tpp) REVERT: C 707 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7536 (tm-30) REVERT: C 722 MET cc_start: 0.4193 (mtm) cc_final: 0.3904 (mtt) REVERT: C 878 ILE cc_start: 0.8036 (tt) cc_final: 0.7794 (tt) outliers start: 23 outliers final: 15 residues processed: 215 average time/residue: 0.1708 time to fit residues: 60.2267 Evaluate side-chains 185 residues out of total 2780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 722 MET Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 870 PHE Chi-restraints excluded: chain B residue 936 GLN Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 349 VAL Chi-restraints excluded: chain C residue 707 GLU Chi-restraints excluded: chain C residue 798 SER Chi-restraints excluded: chain C residue 822 CYS Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 7 optimal weight: 10.0000 chunk 269 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 198 optimal weight: 0.2980 chunk 186 optimal weight: 0.6980 chunk 202 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 290 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 227 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN B 786 GLN B 895 GLN B 917 GLN B 936 GLN ** B 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.260455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.233287 restraints weight = 47012.655| |-----------------------------------------------------------------------------| r_work (start): 0.4707 rms_B_bonded: 2.96 r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5395 moved from start: 1.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 26616 Z= 0.157 Angle : 0.728 23.288 36350 Z= 0.367 Chirality : 0.056 2.004 4264 Planarity : 0.005 0.082 4569 Dihedral : 7.537 113.300 4798 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.76 % Allowed : 14.35 % Favored : 84.89 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: -2.01 (0.14), residues: 3163 helix: -0.17 (0.20), residues: 635 sheet: -0.78 (0.21), residues: 625 loop : -2.03 (0.13), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 48 TYR 0.020 0.001 TYR B 598 PHE 0.034 0.002 PHE C 952 TRP 0.023 0.001 TRP A1084 HIS 0.012 0.001 HIS C 33 Details of bonding type rmsd covalent geometry : bond 0.00348 (26505) covalent geometry : angle 0.68622 (36062) SS BOND : bond 0.00671 ( 45) SS BOND : angle 1.98626 ( 90) hydrogen bonds : bond 0.04530 ( 819) hydrogen bonds : angle 6.06016 ( 2379) link_ALPHA1-3 : bond 0.00443 ( 1) link_ALPHA1-3 : angle 1.51354 ( 3) link_ALPHA1-6 : bond 0.00665 ( 1) link_ALPHA1-6 : angle 1.33080 ( 3) link_BETA1-4 : bond 0.00583 ( 30) link_BETA1-4 : angle 1.49951 ( 90) link_NAG-ASN : bond 0.00693 ( 34) link_NAG-ASN : angle 4.09231 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5328.94 seconds wall clock time: 92 minutes 24.94 seconds (5544.94 seconds total)