Starting phenix.real_space_refine on Sun Sep 13 22:50:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6crw_7574/09_2026/6crw_7574.cif Found real_map, /net/cci-nas-00/data/ceres_data/6crw_7574/09_2026/6crw_7574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6crw_7574/09_2026/6crw_7574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6crw_7574/09_2026/6crw_7574.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6crw_7574/09_2026/6crw_7574.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6crw_7574/09_2026/6crw_7574.cif" model { file = "/net/cci-nas-00/data/ceres_data/6crw_7574/09_2026/6crw_7574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6crw_7574/09_2026/6crw_7574.cif" } resolution = 3.9 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= 0.006 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 16537 2.51 5 N 4192 2.21 5 O 5127 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25994 Number of models: 1 Model: "" Number of chains: 27 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: 8334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8334 Classifications: {'peptide': 1068} Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1014} Chain breaks: 6 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 5.62, per 1000 atoms: 0.22 Number of scatterers: 25994 At special positions: 0 Unit cell: (150.38, 142.14, 175.1, 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 5127 8.00 N 4192 7.00 C 16537 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=2.06 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.02 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=2.55 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=2.03 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=2.02 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.04 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 " " BMA F 3 " - " MAN F 4 " " BMA O 3 " - " MAN O 4 " " BMA R 3 " - " MAN R 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA U 3 " - " MAN U 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 K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1305 " - " ASN A 589 " " NAG A1310 " - " ASN A 691 " " NAG A1317 " - " ASN A1056 " " NAG B1309 " - " ASN B 589 " " NAG B1312 " - " ASN B 691 " " NAG B1322 " - " ASN B1080 " " NAG C1301 " - " ASN C 65 " " NAG C1306 " - " ASN C 227 " " NAG C1309 " - " ASN C 318 " " NAG C1310 " - " ASN C 589 " " NAG C1315 " - " ASN C 691 " " NAG C1324 " - " 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 65 " " NAG K 1 " - " ASN B 269 " " NAG L 1 " - " ASN B 318 " " NAG M 1 " - " ASN B 602 " " NAG N 1 " - " ASN B 699 " " NAG O 1 " - " ASN B 783 " " NAG P 1 " - " ASN B1056 " " NAG Q 1 " - " ASN B1116 " " NAG R 1 " - " ASN C 119 " " NAG S 1 " - " ASN C 269 " " NAG T 1 " - " ASN C 602 " " NAG U 1 " - " ASN C 699 " " NAG V 1 " - " ASN C 783 " " NAG W 1 " - " ASN C1080 " " NAG X 1 " - " ASN C1116 " Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6002 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 52 sheets defined 23.3% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.650A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 371 through 376 removed outlier: 3.778A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 395 removed outlier: 4.309A pdb=" N ARG A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 395' Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.754A pdb=" N TYR A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 602 through 612 removed outlier: 3.688A 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 728 through 736 removed outlier: 3.611A pdb=" N LEU A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 764 removed outlier: 4.010A pdb=" N GLN A 744 " --> pdb=" O SER A 740 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN A 756 " --> pdb=" O ILE A 752 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 809 removed outlier: 3.604A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 removed outlier: 3.516A pdb=" N THR A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 873 removed outlier: 4.265A pdb=" N GLY A 871 " --> pdb=" O GLY A 867 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.189A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 922 Processing helix chain 'A' and resid 927 through 947 removed outlier: 3.682A pdb=" N VAL A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 removed outlier: 4.152A pdb=" N SER A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 1013 removed outlier: 3.775A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA A1002 " --> pdb=" O ALA A 998 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 372 through 377 removed outlier: 3.923A pdb=" N ASP B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 395 removed outlier: 3.947A pdb=" N ARG B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 391 through 395' Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.538A pdb=" N ASP B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.799A pdb=" N THR B 608 " --> pdb=" O THR B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 724 Processing helix chain 'B' and resid 728 through 736 Processing helix chain 'B' and resid 740 through 765 removed outlier: 4.392A pdb=" N GLN B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 809 removed outlier: 3.557A pdb=" N LYS B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 867 removed outlier: 3.737A pdb=" N THR B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 873 Processing helix chain 'B' and resid 879 through 891 removed outlier: 3.919A pdb=" N ILE B 891 " --> pdb=" O ARG B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 900 removed outlier: 4.128A pdb=" N LEU B 898 " --> pdb=" O THR B 894 " (cutoff:3.500A) Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.567A pdb=" N ILE B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 947 removed outlier: 3.539A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN B 937 " --> pdb=" O VAL B 933 " (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 1013 removed outlier: 3.863A pdb=" N VAL B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 980 " --> pdb=" O ASP B 976 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN B 984 " --> pdb=" O THR B 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 372 through 377 removed outlier: 3.742A pdb=" N LEU C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 removed outlier: 3.788A pdb=" N ARG C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.704A pdb=" N TYR C 491 " --> pdb=" O GLY C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 612 removed outlier: 3.504A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 736 removed outlier: 3.572A pdb=" N ALA C 732 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 736 " --> pdb=" O ALA C 732 " (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: 3.784A pdb=" N GLN C 744 " --> pdb=" O SER C 740 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 745 " --> pdb=" O PHE C 741 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 756 " --> pdb=" O ILE C 752 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 805 removed outlier: 3.518A pdb=" N ASP C 802 " --> pdb=" O SER C 798 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C 803 " --> pdb=" O PHE C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 864 Processing helix chain 'C' and resid 867 through 873 removed outlier: 3.820A pdb=" N GLY C 871 " --> pdb=" O GLY C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 Processing helix chain 'C' and resid 895 through 901 Processing helix chain 'C' and resid 901 through 923 Processing helix chain 'C' and resid 927 through 947 removed outlier: 3.630A pdb=" N VAL C 934 " --> pdb=" O LEU C 930 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASN C 937 " --> pdb=" O VAL C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 removed outlier: 3.583A pdb=" N ILE C 962 " --> pdb=" O VAL C 958 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 1015 removed outlier: 3.521A pdb=" N THR C 980 " --> pdb=" O ASP C 976 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 981 " --> pdb=" O ARG C 977 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35 removed outlier: 8.284A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS A 180 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 201 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU A 194 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS A 221 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL A 196 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N TYR A 200 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR A 215 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 9.997A pdb=" N PHE A 213 " --> pdb=" O PRO A 202 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ARG A 38 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 9.154A pdb=" N LEU A 216 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 40 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 3.556A pdb=" N GLY C 534 " --> pdb=" O PHE C 527 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 59 removed outlier: 3.620A pdb=" N ASP A 57 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 260 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N THR A 261 " --> pdb=" O ASP A 277 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N ASP A 277 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N MET A 263 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ALA A 275 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LYS A 265 " --> pdb=" O THR A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.518A pdb=" N TRP A 101 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 123 " --> pdb=" O ILE A 164 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE A 164 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE A 125 " --> pdb=" O GLU A 162 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU A 162 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA A 127 " --> pdb=" O THR A 160 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ASN A 129 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ASN A 158 " --> pdb=" O ASN A 129 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLU A 131 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA A 156 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 149 removed outlier: 3.705A pdb=" N THR A 146 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ALA A 139 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 239 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 615 through 616 removed outlier: 5.136A pdb=" N ILE A 299 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N THR A 585 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLN A 301 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL A 583 " --> pdb=" O GLN A 301 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER A 303 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 581 " --> pdb=" O SER A 303 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 312 through 315 removed outlier: 6.193A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ASP A 560 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 561 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE A 551 " --> pdb=" O PHE B 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 344 through 345 removed outlier: 3.974A pdb=" N CYS A 419 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS A 365 " --> pdb=" O VAL A 420 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB1, first strand: chain 'A' and resid 439 through 441 Processing sheet with id=AB2, first strand: chain 'A' and resid 640 through 646 removed outlier: 6.347A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N VAL A 642 " --> pdb=" O THR A 678 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE A 656 " --> pdb=" O ILE A 652 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 683 through 685 removed outlier: 6.136A 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 694 through 710 removed outlier: 7.104A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 709 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N TYR A1049 " --> pdb=" O HIS A1030 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N HIS A1030 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 710 removed outlier: 7.104A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET A 709 " --> pdb=" O VAL A1042 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A1060 " --> pdb=" O PHE A1077 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A1077 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A1087 " --> pdb=" O VAL A1076 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN A1088 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N SER A1093 " --> pdb=" O GLN A1088 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 717 removed outlier: 4.358A 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 771 removed outlier: 5.997A pdb=" N MET A 770 " --> pdb=" O SER C 685 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AB9, first strand: chain 'A' and resid 822 through 823 Processing sheet with id=AC1, first strand: chain 'A' and resid 1102 through 1107 removed outlier: 3.712A pdb=" N SER A1105 " --> pdb=" O ALA A1069 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA A1069 " --> pdb=" O SER A1105 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ALA A1062 " --> pdb=" O ILE A1115 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 31 through 35 removed outlier: 4.184A pdb=" N LYS B 180 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 31 through 35 Processing sheet with id=AC4, first strand: chain 'B' and resid 51 through 59 removed outlier: 3.577A pdb=" N THR B 51 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 81 through 82 removed outlier: 5.942A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N SER B 239 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL B 140 " --> pdb=" O SER B 239 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA B 139 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 146 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.605A pdb=" N ARG B 126 " --> pdb=" O ILE B 115 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 161 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N ASN B 129 " --> pdb=" O CYS B 159 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N CYS B 159 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 615 through 616 removed outlier: 5.397A pdb=" N ILE B 299 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR B 585 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLN B 301 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 583 " --> pdb=" O GLN B 301 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER B 303 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 581 " --> pdb=" O SER B 303 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 312 through 315 removed outlier: 6.362A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER B 561 " --> pdb=" O GLY B 552 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE B 551 " --> pdb=" O PHE C 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.501A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N CYS B 419 " --> pdb=" O LEU B 499 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.066A pdb=" N CYS B 348 " --> pdb=" O CYS B 511 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 439 through 441 Processing sheet with id=AD3, first strand: chain 'B' and resid 640 through 646 removed outlier: 4.757A pdb=" N THR B 678 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR B 644 " --> pdb=" O THR B 678 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE B 656 " --> pdb=" O ILE B 652 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 683 through 685 removed outlier: 6.161A pdb=" N ALA B 683 " --> pdb=" O MET C 770 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 693 through 696 removed outlier: 3.566A pdb=" N ARG B1055 " --> pdb=" O ILE B 696 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR B1058 " --> pdb=" O PHE B1079 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B1060 " --> pdb=" O PHE B1077 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE B1077 " --> pdb=" O ALA B1060 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 699 through 709 removed outlier: 3.708A pdb=" N SER B 703 " --> pdb=" O THR B1048 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLY B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ALA B1037 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B1043 " --> pdb=" O PRO B1035 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B1045 " --> pdb=" O SER B1033 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N SER B1033 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 716 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 removed outlier: 3.526A pdb=" N ALA B 834 " --> pdb=" O GLU B 821 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1102 through 1107 removed outlier: 5.346A pdb=" N VAL B1104 " --> pdb=" O PHE B1071 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE B1071 " --> pdb=" O VAL B1104 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLY B1106 " --> pdb=" O ALA B1069 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 33 through 35 removed outlier: 7.877A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR C 67 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 254 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 205 " --> pdb=" O PHE C 179 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N HIS C 181 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ILE C 203 " --> pdb=" O HIS C 181 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ARG C 183 " --> pdb=" O GLN C 201 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLN C 201 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE C 185 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLY C 199 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N PHE C 187 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N TYR C 197 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN C 189 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR C 195 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU C 194 " --> pdb=" O LYS C 221 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS C 221 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL C 196 " --> pdb=" O ILE C 219 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 52 through 59 removed outlier: 3.729A pdb=" N THR C 260 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.870A 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: 6.423A pdb=" N VAL C 123 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE C 164 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C 125 " --> pdb=" O GLU C 162 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU C 162 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA C 127 " --> pdb=" O THR C 160 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN C 129 " --> pdb=" O ASN C 158 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ASN C 158 " --> pdb=" O ASN C 129 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLU C 131 " --> pdb=" O ALA C 156 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA C 156 " --> pdb=" O GLU C 131 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N CYS C 133 " --> pdb=" O ASP C 154 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ASP C 154 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASN C 135 " --> pdb=" O ILE C 152 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE C 152 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE C 137 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR C 150 " --> pdb=" O PHE C 137 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA C 139 " --> pdb=" O THR C 148 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 298 through 301 Processing sheet with id=AE6, first strand: chain 'C' and resid 578 through 579 removed outlier: 3.655A pdb=" N GLY C 579 " --> pdb=" O PHE C 305 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.676A pdb=" N VAL C 382 " --> pdb=" O ILE C 345 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 439 through 441 Processing sheet with id=AE9, first strand: chain 'C' and resid 640 through 646 removed outlier: 6.101A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N VAL C 642 " --> pdb=" O THR C 678 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 656 " --> pdb=" O ILE C 652 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 696 through 697 Processing sheet with id=AF2, first strand: chain 'C' and resid 700 through 710 removed outlier: 3.634A pdb=" N MET C1032 " --> pdb=" O VAL C1047 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N TYR C1049 " --> pdb=" O HIS C1030 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N HIS C1030 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AF4, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AF5, first strand: chain 'C' and resid 821 through 823 Processing sheet with id=AF6, first strand: chain 'C' and resid 1058 through 1060 removed outlier: 3.551A pdb=" N THR C1058 " --> pdb=" O PHE C1079 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C1060 " --> pdb=" O PHE C1077 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N PHE C1077 " --> pdb=" O ALA C1060 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1102 through 1107 removed outlier: 3.687A pdb=" N SER C1105 " --> pdb=" O ALA C1069 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ALA C1069 " --> pdb=" O SER C1105 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA C1062 " --> pdb=" O ILE C1115 " (cutoff:3.500A) 964 hydrogen bonds defined for protein. 2643 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.00 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.22: 4 1.22 - 1.38: 9799 1.38 - 1.54: 16450 1.54 - 1.70: 151 1.70 - 1.86: 186 Bond restraints: 26590 Sorted by residual: bond pdb=" C GLN A 737 " pdb=" N TYR A 738 " ideal model delta sigma weight residual 1.333 1.060 0.273 1.37e-02 5.33e+03 3.96e+02 bond pdb=" C LEU A 735 " pdb=" N LEU A 736 " ideal model delta sigma weight residual 1.335 1.553 -0.219 1.25e-02 6.40e+03 3.06e+02 bond pdb=" C LEU A 736 " pdb=" N GLN A 737 " ideal model delta sigma weight residual 1.331 1.566 -0.235 2.56e-02 1.53e+03 8.44e+01 bond pdb=" C1 MAN T 4 " pdb=" O5 MAN T 4 " ideal model delta sigma weight residual 1.399 1.455 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C1 MAN E 4 " pdb=" C2 MAN E 4 " ideal model delta sigma weight residual 1.526 1.581 -0.055 2.00e-02 2.50e+03 7.59e+00 ... (remaining 26585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.08: 36042 5.08 - 10.15: 127 10.15 - 15.23: 6 15.23 - 20.31: 2 20.31 - 25.39: 1 Bond angle restraints: 36178 Sorted by residual: angle pdb=" C GLN A 737 " pdb=" N TYR A 738 " pdb=" CA TYR A 738 " ideal model delta sigma weight residual 121.80 147.19 -25.39 2.16e+00 2.14e-01 1.38e+02 angle pdb=" CA LEU A 736 " pdb=" C LEU A 736 " pdb=" N GLN A 737 " ideal model delta sigma weight residual 116.97 107.28 9.69 1.20e+00 6.94e-01 6.53e+01 angle pdb=" N HIS B 74 " pdb=" CA HIS B 74 " pdb=" C HIS B 74 " ideal model delta sigma weight residual 114.75 106.39 8.36 1.26e+00 6.30e-01 4.41e+01 angle pdb=" CA TYR A 738 " pdb=" C TYR A 738 " pdb=" O TYR A 738 " ideal model delta sigma weight residual 120.31 112.71 7.60 1.25e+00 6.40e-01 3.70e+01 angle pdb=" C GLY B 77 " pdb=" N ASN B 78 " pdb=" CA ASN B 78 " ideal model delta sigma weight residual 122.89 116.18 6.71 1.12e+00 7.97e-01 3.59e+01 ... (remaining 36173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 14710 17.80 - 35.60: 420 35.60 - 53.40: 97 53.40 - 71.20: 7 71.20 - 88.99: 4 Dihedral angle restraints: 15238 sinusoidal: 5907 harmonic: 9331 Sorted by residual: dihedral pdb=" CB CYS A1014 " pdb=" SG CYS A1014 " pdb=" SG CYS A1025 " pdb=" CB CYS A1025 " ideal model delta sinusoidal sigma weight residual 93.00 -178.01 -88.99 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CA ARG C 207 " pdb=" C ARG C 207 " pdb=" N ASP C 208 " pdb=" CA ASP C 208 " ideal model delta harmonic sigma weight residual -180.00 -136.77 -43.23 0 5.00e+00 4.00e-02 7.48e+01 dihedral pdb=" CA ARG B 207 " pdb=" C ARG B 207 " pdb=" N ASP B 208 " pdb=" CA ASP B 208 " ideal model delta harmonic sigma weight residual 180.00 -137.22 -42.78 0 5.00e+00 4.00e-02 7.32e+01 ... (remaining 15235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 3784 0.088 - 0.175: 481 0.175 - 0.263: 19 0.263 - 0.351: 18 0.351 - 0.439: 1 Chirality restraints: 4303 Sorted by residual: chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.25e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.34 -0.06 2.00e-02 2.50e+03 7.92e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN C 119 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 ... (remaining 4300 not shown) Planarity restraints: 4603 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 736 " -0.038 2.00e-02 2.50e+03 7.96e-02 6.33e+01 pdb=" C LEU A 736 " 0.137 2.00e-02 2.50e+03 pdb=" O LEU A 736 " -0.058 2.00e-02 2.50e+03 pdb=" N GLN A 737 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 797 " 0.482 9.50e-02 1.11e+02 2.16e-01 2.88e+01 pdb=" NE ARG A 797 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 797 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG A 797 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 797 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 735 " -0.021 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C LEU A 735 " 0.069 2.00e-02 2.50e+03 pdb=" O LEU A 735 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU A 736 " -0.021 2.00e-02 2.50e+03 ... (remaining 4600 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 44 2.40 - 3.02: 14274 3.02 - 3.65: 37926 3.65 - 4.27: 60361 4.27 - 4.90: 97613 Nonbonded interactions: 210218 Sorted by model distance: nonbonded pdb=" O TYR A 738 " pdb=" OG SER C 950 " model vdw 1.773 3.040 nonbonded pdb=" NH1 ARG C 544 " pdb=" NE2 GLN C 546 " model vdw 1.951 3.200 nonbonded pdb=" O GLY C 77 " pdb=" OH TYR C 252 " model vdw 2.279 3.040 nonbonded pdb=" OD2 ASP C 385 " pdb=" OH TYR C 410 " model vdw 2.289 3.040 nonbonded pdb=" OG SER B 690 " pdb=" OD1 ASN B 692 " model vdw 2.290 3.040 ... (remaining 210213 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 1310)) selection = (chain 'B' and (resid 18 through 366 or resid 371 through 662 or resid 672 throu \ gh 1322)) selection = (chain 'C' and (resid 18 through 662 or resid 672 through 823 or resid 831 throu \ gh 1309)) } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'W' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'O' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 25.880 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.080 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 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 : 0.008 0.523 26709 Z= 0.390 Angle : 1.040 29.250 36490 Z= 0.551 Chirality : 0.059 0.439 4303 Planarity : 0.007 0.216 4569 Dihedral : 9.027 76.749 9101 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.69 % Favored : 94.28 % Rotamer: Outliers : 0.07 % Allowed : 0.90 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.12), residues: 3162 helix: -3.32 (0.12), residues: 643 sheet: -1.38 (0.19), residues: 647 loop : -2.30 (0.12), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 99 TYR 0.030 0.003 TYR B 352 PHE 0.056 0.005 PHE A 501 TRP 0.044 0.003 TRP B 423 HIS 0.016 0.002 HIS C 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00728 / 0.36 (26590) covalent geometry : angle 1.00361 / 0.54 (36178) SS BOND : bond 0.07832 / 6.02 ( 45) SS BOND : angle 3.84727 / 2.60 ( 90) hydrogen bonds : bond 0.26696 / 18.05 ( 939) hydrogen bonds : angle 10.03965 / 7.04 ( 2643) link_ALPHA1-3 : bond 0.00565 / 0.40 ( 6) link_ALPHA1-3 : angle 2.33109 / 1.59 ( 18) link_ALPHA1-6 : bond 0.00299 / 0.16 ( 1) link_ALPHA1-6 : angle 1.39292 / 0.74 ( 3) link_BETA1-4 : bond 0.00668 / 0.43 ( 33) link_BETA1-4 : angle 2.97768 / 2.00 ( 99) link_NAG-ASN : bond 0.00501 / 0.35 ( 34) link_NAG-ASN : angle 2.68221 / 1.76 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 446 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8702 (m-30) cc_final: 0.8397 (p0) REVERT: A 383 TYR cc_start: 0.5013 (m-80) cc_final: 0.4053 (m-80) REVERT: A 417 MET cc_start: 0.2072 (tpt) cc_final: 0.0139 (pmm) REVERT: A 558 PHE cc_start: 0.6648 (t80) cc_final: 0.5378 (t80) REVERT: A 575 PRO cc_start: 0.7952 (Cg_exo) cc_final: 0.7378 (Cg_endo) REVERT: A 978 LEU cc_start: 0.9044 (tp) cc_final: 0.8837 (pp) REVERT: B 92 THR cc_start: 0.7371 (p) cc_final: 0.7155 (p) REVERT: B 107 MET cc_start: 0.1777 (mmt) cc_final: 0.1446 (mmt) REVERT: B 214 ASN cc_start: 0.7239 (t0) cc_final: 0.7026 (m-40) REVERT: B 417 MET cc_start: 0.2779 (ttt) cc_final: 0.2238 (mmm) REVERT: B 515 LEU cc_start: 0.6905 (tp) cc_final: 0.6026 (pp) REVERT: C 151 MET cc_start: 0.5131 (mmt) cc_final: 0.4889 (mtt) REVERT: C 266 TYR cc_start: 0.7557 (m-10) cc_final: 0.7332 (m-10) REVERT: C 312 ASP cc_start: 0.6683 (t0) cc_final: 0.6315 (m-30) REVERT: C 329 PHE cc_start: 0.3892 (m-80) cc_final: 0.2744 (m-10) REVERT: C 347 ASN cc_start: 0.8313 (m-40) cc_final: 0.7774 (p0) REVERT: C 1059 THR cc_start: 0.7953 (p) cc_final: 0.7717 (p) outliers start: 2 outliers final: 0 residues processed: 447 average time/residue: 0.1856 time to fit residues: 126.6652 Evaluate side-chains 212 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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: 7.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.4980 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS A 692 ASN A 721 ASN A 733 ASN A 877 GLN ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 937 ASN A 984 GLN A 993 GLN A1088 GLN B 32 GLN B 70 HIS B 112 GLN B 118 ASN B 149 HIS B 201 GLN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 ASN B 907 ASN B 984 GLN B1065 HIS C 149 HIS C 201 GLN C 599 GLN C 733 ASN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.117761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.090508 restraints weight = 114140.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.090769 restraints weight = 81293.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.090390 restraints weight = 67297.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.090904 restraints weight = 66410.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.090917 restraints weight = 56578.411| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 26709 Z= 0.210 Angle : 0.767 14.509 36490 Z= 0.396 Chirality : 0.047 0.231 4303 Planarity : 0.006 0.059 4569 Dihedral : 6.165 34.767 3437 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.51 % Allowed : 6.48 % Favored : 92.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.14), residues: 3162 helix: -0.58 (0.19), residues: 655 sheet: -0.91 (0.19), residues: 672 loop : -2.01 (0.13), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 965 TYR 0.024 0.002 TYR B1029 PHE 0.026 0.002 PHE A 83 TRP 0.021 0.002 TRP B 340 HIS 0.004 0.001 HIS B1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (26590) covalent geometry : angle 0.75086 / 0.39 (36178) SS BOND : bond 0.00427 / 0.26 ( 45) SS BOND : angle 1.64148 / 1.10 ( 90) hydrogen bonds : bond 0.05943 / 3.98 ( 939) hydrogen bonds : angle 6.86143 / 4.80 ( 2643) link_ALPHA1-3 : bond 0.00394 / 0.28 ( 6) link_ALPHA1-3 : angle 1.71360 / 1.19 ( 18) link_ALPHA1-6 : bond 0.00498 / 0.26 ( 1) link_ALPHA1-6 : angle 1.24815 / 0.70 ( 3) link_BETA1-4 : bond 0.00401 / 0.26 ( 33) link_BETA1-4 : angle 1.95545 / 1.38 ( 99) link_NAG-ASN : bond 0.00231 / 0.15 ( 34) link_NAG-ASN : angle 1.94693 / 1.30 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 232 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7117 (OUTLIER) cc_final: 0.6491 (ppp) REVERT: A 166 ASP cc_start: 0.8813 (m-30) cc_final: 0.8444 (p0) REVERT: A 383 TYR cc_start: 0.5670 (m-80) cc_final: 0.4645 (m-80) REVERT: A 417 MET cc_start: 0.2296 (tpt) cc_final: 0.0136 (pmm) REVERT: A 494 TYR cc_start: 0.7041 (m-80) cc_final: 0.6813 (m-80) REVERT: A 952 PHE cc_start: 0.7429 (m-80) cc_final: 0.7020 (m-80) REVERT: A 978 LEU cc_start: 0.9011 (tp) cc_final: 0.8774 (pp) REVERT: B 37 MET cc_start: 0.7907 (mmp) cc_final: 0.7439 (mmp) REVERT: B 107 MET cc_start: 0.3310 (mmt) cc_final: 0.3026 (mmt) REVERT: B 214 ASN cc_start: 0.7234 (t0) cc_final: 0.6985 (m-40) REVERT: B 417 MET cc_start: 0.3035 (ttt) cc_final: 0.2388 (mmm) REVERT: B 515 LEU cc_start: 0.6930 (tp) cc_final: 0.6640 (pp) REVERT: B 708 VAL cc_start: 0.9308 (t) cc_final: 0.9015 (m) REVERT: B 976 ASP cc_start: 0.7445 (m-30) cc_final: 0.7225 (m-30) REVERT: C 224 LEU cc_start: 0.8087 (mt) cc_final: 0.7802 (mt) REVERT: C 296 ASP cc_start: 0.8241 (m-30) cc_final: 0.7975 (m-30) REVERT: C 312 ASP cc_start: 0.6813 (t0) cc_final: 0.6268 (m-30) REVERT: C 329 PHE cc_start: 0.4167 (m-80) cc_final: 0.3340 (m-10) REVERT: C 347 ASN cc_start: 0.8632 (m-40) cc_final: 0.7990 (p0) REVERT: C 383 TYR cc_start: 0.3932 (OUTLIER) cc_final: 0.3478 (m-10) REVERT: C 936 GLN cc_start: 0.8599 (mm110) cc_final: 0.8043 (mm-40) REVERT: C 1066 GLU cc_start: 0.7251 (mt-10) cc_final: 0.6675 (tt0) outliers start: 42 outliers final: 21 residues processed: 261 average time/residue: 0.1482 time to fit residues: 64.2048 Evaluate side-chains 211 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 937 ASN Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 383 TYR Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1009 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 293 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 138 optimal weight: 30.0000 chunk 265 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 307 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 168 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 835 GLN ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN C 599 GLN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.116631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.089085 restraints weight = 116065.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.090077 restraints weight = 78826.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.089563 restraints weight = 70170.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.090295 restraints weight = 60671.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.090412 restraints weight = 50468.639| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 26709 Z= 0.173 Angle : 0.689 14.992 36490 Z= 0.349 Chirality : 0.045 0.232 4303 Planarity : 0.005 0.046 4569 Dihedral : 5.708 32.158 3437 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.80 % Allowed : 7.99 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.14), residues: 3162 helix: 0.23 (0.20), residues: 656 sheet: -0.96 (0.19), residues: 685 loop : -1.89 (0.13), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 563 TYR 0.020 0.002 TYR B 989 PHE 0.029 0.002 PHE C 334 TRP 0.027 0.002 TRP C 245 HIS 0.005 0.001 HIS C 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 (26590) covalent geometry : angle 0.67428 / 0.35 (36178) SS BOND : bond 0.00500 / 0.30 ( 45) SS BOND : angle 1.51854 / 0.99 ( 90) hydrogen bonds : bond 0.04873 / 3.24 ( 939) hydrogen bonds : angle 6.28930 / 4.39 ( 2643) link_ALPHA1-3 : bond 0.00618 / 0.40 ( 6) link_ALPHA1-3 : angle 1.76287 / 1.23 ( 18) link_ALPHA1-6 : bond 0.00571 / 0.30 ( 1) link_ALPHA1-6 : angle 1.29432 / 0.72 ( 3) link_BETA1-4 : bond 0.00401 / 0.26 ( 33) link_BETA1-4 : angle 1.71403 / 1.20 ( 99) link_NAG-ASN : bond 0.00177 / 0.13 ( 34) link_NAG-ASN : angle 1.72318 / 1.14 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7154 (OUTLIER) cc_final: 0.6926 (ppp) REVERT: A 166 ASP cc_start: 0.8805 (m-30) cc_final: 0.8425 (p0) REVERT: A 383 TYR cc_start: 0.5731 (m-80) cc_final: 0.4709 (m-80) REVERT: A 417 MET cc_start: 0.2266 (tpt) cc_final: 0.0462 (ptp) REVERT: A 494 TYR cc_start: 0.7178 (m-80) cc_final: 0.6815 (m-80) REVERT: A 918 GLU cc_start: 0.8114 (tp30) cc_final: 0.7902 (tp30) REVERT: A 952 PHE cc_start: 0.7594 (m-80) cc_final: 0.7174 (m-80) REVERT: A 978 LEU cc_start: 0.9005 (tp) cc_final: 0.8730 (pp) REVERT: B 214 ASN cc_start: 0.7240 (t0) cc_final: 0.6999 (m-40) REVERT: B 417 MET cc_start: 0.2784 (ttt) cc_final: 0.2325 (mmm) REVERT: B 515 LEU cc_start: 0.6956 (tp) cc_final: 0.6702 (pp) REVERT: C 224 LEU cc_start: 0.8300 (mt) cc_final: 0.8018 (mt) REVERT: C 296 ASP cc_start: 0.8224 (m-30) cc_final: 0.7924 (m-30) REVERT: C 329 PHE cc_start: 0.4264 (m-80) cc_final: 0.3281 (m-10) REVERT: C 347 ASN cc_start: 0.8588 (m-40) cc_final: 0.7884 (p0) REVERT: C 576 CYS cc_start: 0.6330 (OUTLIER) cc_final: 0.5965 (t) REVERT: C 722 MET cc_start: 0.8268 (tpp) cc_final: 0.8020 (tpt) REVERT: C 936 GLN cc_start: 0.8596 (mm110) cc_final: 0.8091 (mm-40) REVERT: C 967 ASP cc_start: 0.8854 (p0) cc_final: 0.8531 (p0) outliers start: 50 outliers final: 28 residues processed: 243 average time/residue: 0.1472 time to fit residues: 60.9889 Evaluate side-chains 202 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 548 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 164 ILE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1085 PHE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 694 ILE Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1009 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 3 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 218 optimal weight: 0.8980 chunk 107 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 121 optimal weight: 30.0000 chunk 297 optimal weight: 0.7980 chunk 244 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 630 GLN A 661 HIS A 692 ASN ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 HIS ** B 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN B1088 GLN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.117690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.089246 restraints weight = 114281.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.090539 restraints weight = 78506.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.090854 restraints weight = 55224.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.091424 restraints weight = 48825.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.091339 restraints weight = 43645.958| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 26709 Z= 0.122 Angle : 0.635 16.152 36490 Z= 0.319 Chirality : 0.044 0.211 4303 Planarity : 0.004 0.042 4569 Dihedral : 5.330 32.618 3437 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.73 % Allowed : 8.53 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.14), residues: 3162 helix: 0.77 (0.21), residues: 648 sheet: -0.89 (0.19), residues: 686 loop : -1.81 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 965 TYR 0.023 0.001 TYR B 197 PHE 0.033 0.002 PHE C 334 TRP 0.016 0.001 TRP B 423 HIS 0.003 0.001 HIS C 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (26590) covalent geometry : angle 0.61875 / 0.31 (36178) SS BOND : bond 0.00343 / 0.18 ( 45) SS BOND : angle 1.92259 / 1.20 ( 90) hydrogen bonds : bond 0.04216 / 2.80 ( 939) hydrogen bonds : angle 5.89713 / 4.13 ( 2643) link_ALPHA1-3 : bond 0.00631 / 0.38 ( 6) link_ALPHA1-3 : angle 1.62435 / 1.11 ( 18) link_ALPHA1-6 : bond 0.00536 / 0.28 ( 1) link_ALPHA1-6 : angle 1.32878 / 0.74 ( 3) link_BETA1-4 : bond 0.00382 / 0.24 ( 33) link_BETA1-4 : angle 1.55762 / 1.10 ( 99) link_NAG-ASN : bond 0.00153 / 0.11 ( 34) link_NAG-ASN : angle 1.52984 / 1.01 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ASN cc_start: 0.7088 (t0) cc_final: 0.6880 (t0) REVERT: A 146 THR cc_start: 0.6109 (OUTLIER) cc_final: 0.5779 (t) REVERT: A 166 ASP cc_start: 0.8800 (m-30) cc_final: 0.8495 (p0) REVERT: A 417 MET cc_start: 0.2036 (tpt) cc_final: 0.0412 (ptp) REVERT: A 494 TYR cc_start: 0.7363 (m-80) cc_final: 0.6999 (m-80) REVERT: A 600 ASP cc_start: 0.8136 (p0) cc_final: 0.7824 (t70) REVERT: A 713 MET cc_start: 0.7603 (tpp) cc_final: 0.7137 (tpt) REVERT: A 918 GLU cc_start: 0.8110 (tp30) cc_final: 0.7847 (tp30) REVERT: A 952 PHE cc_start: 0.7660 (m-80) cc_final: 0.7223 (m-80) REVERT: A 978 LEU cc_start: 0.8914 (tp) cc_final: 0.8660 (pp) REVERT: B 37 MET cc_start: 0.7885 (mmp) cc_final: 0.7483 (mmp) REVERT: B 214 ASN cc_start: 0.7240 (t0) cc_final: 0.7003 (m110) REVERT: B 265 LYS cc_start: 0.9127 (tttt) cc_final: 0.8892 (tptp) REVERT: B 515 LEU cc_start: 0.6936 (tp) cc_final: 0.6683 (pp) REVERT: C 296 ASP cc_start: 0.8111 (m-30) cc_final: 0.7864 (m-30) REVERT: C 329 PHE cc_start: 0.4424 (m-80) cc_final: 0.3424 (m-10) REVERT: C 347 ASN cc_start: 0.8647 (m-40) cc_final: 0.7965 (p0) REVERT: C 576 CYS cc_start: 0.6199 (OUTLIER) cc_final: 0.5824 (t) REVERT: C 722 MET cc_start: 0.8158 (tpp) cc_final: 0.7817 (tpt) REVERT: C 738 TYR cc_start: 0.7154 (m-80) cc_final: 0.6736 (m-80) REVERT: C 884 MET cc_start: 0.8264 (tpp) cc_final: 0.8028 (tpp) REVERT: C 936 GLN cc_start: 0.8581 (mm110) cc_final: 0.8097 (mm-40) outliers start: 48 outliers final: 25 residues processed: 232 average time/residue: 0.1461 time to fit residues: 57.2494 Evaluate side-chains 213 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1085 PHE Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 22 PHE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 741 PHE Chi-restraints excluded: chain C residue 963 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 30 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 9 optimal weight: 50.0000 chunk 123 optimal weight: 20.0000 chunk 293 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 127 optimal weight: 20.0000 chunk 268 optimal weight: 6.9990 chunk 226 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 122 ASN ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN A 280 GLN A 661 HIS A 692 ASN A 786 GLN ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 641 HIS B 896 ASN B 987 GLN B 992 GLN ** C 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 ASN C 147 GLN C 599 GLN C 993 GLN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.113012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.088415 restraints weight = 127807.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.086954 restraints weight = 100000.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.087318 restraints weight = 86551.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.087573 restraints weight = 79120.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.087714 restraints weight = 67849.331| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.115 26709 Z= 0.331 Angle : 0.867 14.500 36490 Z= 0.436 Chirality : 0.050 0.289 4303 Planarity : 0.005 0.058 4569 Dihedral : 6.055 32.680 3437 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.20 % Allowed : 10.72 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.14), residues: 3162 helix: -0.24 (0.19), residues: 681 sheet: -1.21 (0.19), residues: 666 loop : -2.09 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 996 TYR 0.048 0.003 TYR B 197 PHE 0.038 0.003 PHE A 83 TRP 0.017 0.002 TRP A 619 HIS 0.009 0.002 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.33 (26590) covalent geometry : angle 0.84742 / 0.43 (36178) SS BOND : bond 0.00644 / 0.45 ( 45) SS BOND : angle 2.14475 / 1.36 ( 90) hydrogen bonds : bond 0.05451 / 3.62 ( 939) hydrogen bonds : angle 6.60439 / 4.60 ( 2643) link_ALPHA1-3 : bond 0.00565 / 0.37 ( 6) link_ALPHA1-3 : angle 1.98930 / 1.48 ( 18) link_ALPHA1-6 : bond 0.00639 / 0.34 ( 1) link_ALPHA1-6 : angle 1.20039 / 0.68 ( 3) link_BETA1-4 : bond 0.00442 / 0.28 ( 33) link_BETA1-4 : angle 1.98330 / 1.38 ( 99) link_NAG-ASN : bond 0.00622 / 0.42 ( 34) link_NAG-ASN : angle 2.31585 / 1.51 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 169 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8786 (m-30) cc_final: 0.8300 (p0) REVERT: A 197 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: A 417 MET cc_start: 0.2463 (tpt) cc_final: 0.0834 (ptp) REVERT: A 738 TYR cc_start: 0.6195 (OUTLIER) cc_final: 0.5577 (m-80) REVERT: A 976 ASP cc_start: 0.7518 (t0) cc_final: 0.7266 (t70) REVERT: A 978 LEU cc_start: 0.9148 (tp) cc_final: 0.8897 (tt) REVERT: B 214 ASN cc_start: 0.7081 (t0) cc_final: 0.6823 (m110) REVERT: B 515 LEU cc_start: 0.7179 (tp) cc_final: 0.6866 (pp) REVERT: B 916 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9088 (tt) REVERT: B 1013 GLU cc_start: 0.7775 (mm-30) cc_final: 0.7302 (mm-30) REVERT: C 296 ASP cc_start: 0.8065 (m-30) cc_final: 0.7742 (m-30) REVERT: C 329 PHE cc_start: 0.4868 (m-80) cc_final: 0.4108 (m-10) REVERT: C 576 CYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5758 (t) REVERT: C 884 MET cc_start: 0.8276 (tpp) cc_final: 0.8074 (tpp) outliers start: 61 outliers final: 36 residues processed: 213 average time/residue: 0.1381 time to fit residues: 50.7881 Evaluate side-chains 194 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 197 TYR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 709 MET Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1085 PHE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 103 PHE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1111 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 741 PHE Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1019 SER Chi-restraints excluded: chain C residue 1059 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 166 optimal weight: 2.9990 chunk 147 optimal weight: 40.0000 chunk 288 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 chunk 306 optimal weight: 0.9980 chunk 146 optimal weight: 0.3980 chunk 223 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 118 ASN A 661 HIS ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 947 GLN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 987 GLN C 599 GLN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.115351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.089079 restraints weight = 114847.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.088657 restraints weight = 79040.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.088691 restraints weight = 67099.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.089142 restraints weight = 63561.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.089251 restraints weight = 54003.306| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26709 Z= 0.135 Angle : 0.668 16.058 36490 Z= 0.333 Chirality : 0.045 0.238 4303 Planarity : 0.004 0.045 4569 Dihedral : 5.505 31.285 3437 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.66 % Allowed : 11.69 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3162 helix: 0.56 (0.20), residues: 674 sheet: -1.00 (0.19), residues: 683 loop : -1.96 (0.13), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 996 TYR 0.041 0.001 TYR B 197 PHE 0.031 0.002 PHE A 83 TRP 0.016 0.001 TRP B 868 HIS 0.004 0.001 HIS A1030 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (26590) covalent geometry : angle 0.65250 / 0.33 (36178) SS BOND : bond 0.00371 / 0.21 ( 45) SS BOND : angle 1.87009 / 1.18 ( 90) hydrogen bonds : bond 0.04262 / 2.82 ( 939) hydrogen bonds : angle 5.90827 / 4.13 ( 2643) link_ALPHA1-3 : bond 0.00704 / 0.45 ( 6) link_ALPHA1-3 : angle 1.66840 / 1.14 ( 18) link_ALPHA1-6 : bond 0.00632 / 0.33 ( 1) link_ALPHA1-6 : angle 1.31306 / 0.72 ( 3) link_BETA1-4 : bond 0.00391 / 0.25 ( 33) link_BETA1-4 : angle 1.52879 / 1.08 ( 99) link_NAG-ASN : bond 0.00165 / 0.12 ( 34) link_NAG-ASN : angle 1.62239 / 1.02 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 193 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.8841 (m-30) cc_final: 0.8486 (p0) REVERT: A 417 MET cc_start: 0.2002 (tpt) cc_final: 0.0980 (ptp) REVERT: A 738 TYR cc_start: 0.5790 (OUTLIER) cc_final: 0.5530 (m-80) REVERT: A 918 GLU cc_start: 0.8279 (tp30) cc_final: 0.8004 (tp30) REVERT: A 952 PHE cc_start: 0.7874 (m-80) cc_final: 0.7226 (m-80) REVERT: A 975 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7709 (tt) REVERT: A 976 ASP cc_start: 0.7558 (t0) cc_final: 0.7310 (t70) REVERT: A 978 LEU cc_start: 0.9059 (tp) cc_final: 0.8763 (pp) REVERT: B 37 MET cc_start: 0.8034 (mmp) cc_final: 0.7568 (mmp) REVERT: B 515 LEU cc_start: 0.7041 (tp) cc_final: 0.6801 (pp) REVERT: B 916 ILE cc_start: 0.9467 (tp) cc_final: 0.9148 (tt) REVERT: C 296 ASP cc_start: 0.8327 (m-30) cc_final: 0.8040 (m-30) REVERT: C 329 PHE cc_start: 0.4776 (m-80) cc_final: 0.4027 (m-10) REVERT: C 347 ASN cc_start: 0.8546 (m-40) cc_final: 0.7831 (p0) REVERT: C 543 LYS cc_start: 0.8181 (mttm) cc_final: 0.7965 (mmtm) REVERT: C 576 CYS cc_start: 0.6338 (OUTLIER) cc_final: 0.6006 (t) REVERT: C 884 MET cc_start: 0.8470 (tpp) cc_final: 0.8253 (tpp) REVERT: C 936 GLN cc_start: 0.8744 (mm110) cc_final: 0.8292 (mm-40) outliers start: 46 outliers final: 29 residues processed: 228 average time/residue: 0.1446 time to fit residues: 56.2168 Evaluate side-chains 197 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 975 ILE Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1059 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 267 optimal weight: 7.9990 chunk 127 optimal weight: 20.0000 chunk 16 optimal weight: 30.0000 chunk 133 optimal weight: 1.9990 chunk 283 optimal weight: 4.9990 chunk 167 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1117 ASN B 112 GLN B 201 GLN ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN B 992 GLN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** 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 = 0.4167 r_free = 0.4167 target = 0.114407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.087751 restraints weight = 114542.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.087331 restraints weight = 79478.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.087488 restraints weight = 66703.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.087821 restraints weight = 63413.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.088130 restraints weight = 52851.255| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 26709 Z= 0.170 Angle : 0.680 15.147 36490 Z= 0.339 Chirality : 0.045 0.230 4303 Planarity : 0.004 0.042 4569 Dihedral : 5.420 31.036 3437 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.02 % Allowed : 12.45 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.14), residues: 3162 helix: 0.63 (0.20), residues: 680 sheet: -1.01 (0.19), residues: 667 loop : -1.99 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 996 TYR 0.038 0.002 TYR B 197 PHE 0.030 0.002 PHE A 83 TRP 0.015 0.001 TRP B 423 HIS 0.005 0.001 HIS C 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (26590) covalent geometry : angle 0.66521 / 0.33 (36178) SS BOND : bond 0.00397 / 0.23 ( 45) SS BOND : angle 1.80070 / 1.14 ( 90) hydrogen bonds : bond 0.04203 / 2.78 ( 939) hydrogen bonds : angle 5.86100 / 4.08 ( 2643) link_ALPHA1-3 : bond 0.00640 / 0.40 ( 6) link_ALPHA1-3 : angle 1.70506 / 1.22 ( 18) link_ALPHA1-6 : bond 0.00631 / 0.33 ( 1) link_ALPHA1-6 : angle 1.27854 / 0.71 ( 3) link_BETA1-4 : bond 0.00379 / 0.24 ( 33) link_BETA1-4 : angle 1.56175 / 1.10 ( 99) link_NAG-ASN : bond 0.00238 / 0.16 ( 34) link_NAG-ASN : angle 1.69814 / 1.09 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 0.972 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 166 ASP cc_start: 0.8833 (m-30) cc_final: 0.8465 (p0) REVERT: A 417 MET cc_start: 0.2209 (tpt) cc_final: 0.1435 (mpp) REVERT: A 545 PHE cc_start: 0.4003 (OUTLIER) cc_final: 0.3121 (m-10) REVERT: A 738 TYR cc_start: 0.6025 (OUTLIER) cc_final: 0.5781 (m-80) REVERT: A 952 PHE cc_start: 0.7871 (m-80) cc_final: 0.7375 (m-80) REVERT: A 976 ASP cc_start: 0.7588 (t0) cc_final: 0.7290 (t70) REVERT: B 515 LEU cc_start: 0.7175 (tp) cc_final: 0.6959 (pp) REVERT: B 916 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9137 (tt) REVERT: B 1011 MET cc_start: 0.8662 (tpp) cc_final: 0.7592 (mpp) REVERT: B 1013 GLU cc_start: 0.7534 (mm-30) cc_final: 0.6962 (mm-30) REVERT: C 151 MET cc_start: 0.4576 (mpp) cc_final: 0.3763 (ptp) REVERT: C 217 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8129 (mtmm) REVERT: C 296 ASP cc_start: 0.8124 (m-30) cc_final: 0.7798 (m-30) REVERT: C 329 PHE cc_start: 0.5003 (m-80) cc_final: 0.4305 (m-10) REVERT: C 347 ASN cc_start: 0.8483 (m-40) cc_final: 0.7755 (p0) REVERT: C 576 CYS cc_start: 0.6309 (OUTLIER) cc_final: 0.5905 (t) REVERT: C 884 MET cc_start: 0.8295 (tpp) cc_final: 0.8039 (tpp) REVERT: C 936 GLN cc_start: 0.8676 (mm110) cc_final: 0.8278 (mm-40) outliers start: 56 outliers final: 36 residues processed: 220 average time/residue: 0.1392 time to fit residues: 52.2222 Evaluate side-chains 202 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 916 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1059 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 312 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 59 optimal weight: 0.0770 chunk 145 optimal weight: 20.0000 chunk 301 optimal weight: 6.9990 chunk 216 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 316 optimal weight: 7.9990 chunk 119 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN B 992 GLN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.112825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.086269 restraints weight = 117449.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.086289 restraints weight = 84816.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.086214 restraints weight = 68736.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.086556 restraints weight = 67757.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.086630 restraints weight = 57239.396| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 26709 Z= 0.230 Angle : 0.749 15.274 36490 Z= 0.373 Chirality : 0.046 0.249 4303 Planarity : 0.005 0.046 4569 Dihedral : 5.641 31.358 3437 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.16 % Allowed : 12.70 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.14), residues: 3162 helix: 0.35 (0.20), residues: 686 sheet: -1.08 (0.20), residues: 648 loop : -2.08 (0.13), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 761 TYR 0.045 0.002 TYR B 197 PHE 0.035 0.002 PHE A 83 TRP 0.019 0.002 TRP B 868 HIS 0.006 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.23 (26590) covalent geometry : angle 0.73257 / 0.37 (36178) SS BOND : bond 0.00510 / 0.31 ( 45) SS BOND : angle 1.89226 / 1.21 ( 90) hydrogen bonds : bond 0.04538 / 3.01 ( 939) hydrogen bonds : angle 6.08973 / 4.23 ( 2643) link_ALPHA1-3 : bond 0.00633 / 0.40 ( 6) link_ALPHA1-3 : angle 1.75622 / 1.27 ( 18) link_ALPHA1-6 : bond 0.00713 / 0.38 ( 1) link_ALPHA1-6 : angle 1.23725 / 0.69 ( 3) link_BETA1-4 : bond 0.00399 / 0.25 ( 33) link_BETA1-4 : angle 1.67755 / 1.18 ( 99) link_NAG-ASN : bond 0.00353 / 0.24 ( 34) link_NAG-ASN : angle 1.90855 / 1.23 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 158 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.5994 (ptm) cc_final: 0.5189 (tmm) REVERT: A 166 ASP cc_start: 0.8772 (m-30) cc_final: 0.8366 (p0) REVERT: A 417 MET cc_start: 0.2139 (tpt) cc_final: 0.1448 (mpp) REVERT: A 545 PHE cc_start: 0.4212 (OUTLIER) cc_final: 0.3470 (m-10) REVERT: A 738 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.5760 (m-80) REVERT: A 952 PHE cc_start: 0.8012 (m-80) cc_final: 0.7748 (m-80) REVERT: A 976 ASP cc_start: 0.7932 (t0) cc_final: 0.7247 (t70) REVERT: A 984 GLN cc_start: 0.8392 (tm-30) cc_final: 0.7787 (tm-30) REVERT: B 515 LEU cc_start: 0.7264 (tp) cc_final: 0.7043 (pp) REVERT: B 916 ILE cc_start: 0.9564 (tp) cc_final: 0.9249 (tt) REVERT: B 1011 MET cc_start: 0.8884 (tpp) cc_final: 0.8313 (tpp) REVERT: B 1013 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7153 (mm-30) REVERT: B 1018 GLN cc_start: 0.4525 (tp40) cc_final: 0.3772 (tp-100) REVERT: C 217 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8223 (mtmm) REVERT: C 296 ASP cc_start: 0.8363 (m-30) cc_final: 0.8044 (m-30) REVERT: C 329 PHE cc_start: 0.4713 (m-80) cc_final: 0.4099 (m-10) REVERT: C 576 CYS cc_start: 0.6557 (OUTLIER) cc_final: 0.6231 (t) REVERT: C 884 MET cc_start: 0.8513 (tpp) cc_final: 0.8283 (tpp) outliers start: 60 outliers final: 42 residues processed: 201 average time/residue: 0.1350 time to fit residues: 47.0169 Evaluate side-chains 200 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 870 PHE Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1022 VAL Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 752 ILE Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 741 PHE Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1009 THR Chi-restraints excluded: chain C residue 1059 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 202 optimal weight: 0.8980 chunk 227 optimal weight: 6.9990 chunk 277 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 226 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 216 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 178 optimal weight: 0.8980 chunk 46 optimal weight: 30.0000 chunk 164 optimal weight: 9.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 661 HIS ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN B1088 GLN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.115041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.089104 restraints weight = 115707.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.088948 restraints weight = 84362.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.088948 restraints weight = 70316.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.089375 restraints weight = 66492.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.089651 restraints weight = 55761.669| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26709 Z= 0.120 Angle : 0.661 16.009 36490 Z= 0.326 Chirality : 0.044 0.212 4303 Planarity : 0.004 0.043 4569 Dihedral : 5.292 37.518 3437 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.58 % Allowed : 13.49 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3162 helix: 0.81 (0.21), residues: 686 sheet: -0.85 (0.20), residues: 639 loop : -2.03 (0.13), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 761 TYR 0.044 0.001 TYR B 197 PHE 0.046 0.002 PHE B 179 TRP 0.019 0.001 TRP B 868 HIS 0.008 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (26590) covalent geometry : angle 0.64805 / 0.32 (36178) SS BOND : bond 0.00382 / 0.20 ( 45) SS BOND : angle 1.76160 / 1.10 ( 90) hydrogen bonds : bond 0.03921 / 2.59 ( 939) hydrogen bonds : angle 5.67029 / 3.95 ( 2643) link_ALPHA1-3 : bond 0.00643 / 0.41 ( 6) link_ALPHA1-3 : angle 1.53158 / 1.07 ( 18) link_ALPHA1-6 : bond 0.00557 / 0.29 ( 1) link_ALPHA1-6 : angle 1.31789 / 0.73 ( 3) link_BETA1-4 : bond 0.00387 / 0.25 ( 33) link_BETA1-4 : angle 1.42618 / 1.01 ( 99) link_NAG-ASN : bond 0.00128 / 0.09 ( 34) link_NAG-ASN : angle 1.51839 / 0.96 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 182 time to evaluate : 0.966 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 166 ASP cc_start: 0.8829 (m-30) cc_final: 0.8479 (p0) REVERT: A 417 MET cc_start: 0.2002 (tpt) cc_final: 0.1494 (mpp) REVERT: A 545 PHE cc_start: 0.3967 (OUTLIER) cc_final: 0.3061 (m-10) REVERT: A 738 TYR cc_start: 0.5915 (OUTLIER) cc_final: 0.5496 (m-80) REVERT: A 918 GLU cc_start: 0.8303 (tp30) cc_final: 0.8015 (tp30) REVERT: A 952 PHE cc_start: 0.8008 (m-80) cc_final: 0.7751 (m-80) REVERT: A 976 ASP cc_start: 0.7851 (t0) cc_final: 0.7181 (t70) REVERT: A 977 ARG cc_start: 0.8942 (ttm-80) cc_final: 0.8339 (mtm110) REVERT: A 984 GLN cc_start: 0.8413 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 56 GLN cc_start: 0.8557 (mp10) cc_final: 0.7658 (pt0) REVERT: B 179 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6632 (t80) REVERT: B 515 LEU cc_start: 0.7170 (tp) cc_final: 0.6946 (pp) REVERT: B 916 ILE cc_start: 0.9528 (tp) cc_final: 0.9171 (tt) REVERT: B 1011 MET cc_start: 0.8802 (tpp) cc_final: 0.8207 (tpp) REVERT: B 1013 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7210 (mm-30) REVERT: C 151 MET cc_start: 0.6030 (mpp) cc_final: 0.4090 (mpp) REVERT: C 217 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8192 (mtmm) REVERT: C 296 ASP cc_start: 0.8197 (m-30) cc_final: 0.7901 (m-30) REVERT: C 329 PHE cc_start: 0.4162 (m-80) cc_final: 0.3374 (m-10) REVERT: C 347 ASN cc_start: 0.8419 (m-40) cc_final: 0.7635 (p0) REVERT: C 576 CYS cc_start: 0.6207 (OUTLIER) cc_final: 0.5810 (t) REVERT: C 600 ASP cc_start: 0.8214 (m-30) cc_final: 0.7667 (m-30) REVERT: C 884 MET cc_start: 0.8503 (tpp) cc_final: 0.8219 (tpp) REVERT: C 936 GLN cc_start: 0.8757 (mm110) cc_final: 0.8261 (mm-40) outliers start: 44 outliers final: 31 residues processed: 215 average time/residue: 0.1515 time to fit residues: 54.5010 Evaluate side-chains 207 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 171 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 576 CYS Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 731 CYS Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1059 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 290 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 239 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 293 optimal weight: 8.9990 chunk 266 optimal weight: 1.9990 chunk 240 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 721 ASN ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN B 992 GLN ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.114133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.087759 restraints weight = 115227.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.087626 restraints weight = 84136.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.087514 restraints weight = 66988.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.087913 restraints weight = 65485.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.088086 restraints weight = 57808.743| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 26709 Z= 0.162 Angle : 0.689 15.669 36490 Z= 0.340 Chirality : 0.045 0.256 4303 Planarity : 0.004 0.048 4569 Dihedral : 5.281 33.572 3437 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.62 % Allowed : 13.75 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.14), residues: 3162 helix: 0.74 (0.20), residues: 683 sheet: -0.94 (0.20), residues: 645 loop : -2.01 (0.13), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 306 TYR 0.046 0.002 TYR B 197 PHE 0.042 0.002 PHE B 179 TRP 0.015 0.001 TRP B 868 HIS 0.009 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (26590) covalent geometry : angle 0.67549 / 0.34 (36178) SS BOND : bond 0.00554 / 0.34 ( 45) SS BOND : angle 1.75605 / 1.12 ( 90) hydrogen bonds : bond 0.04062 / 2.71 ( 939) hydrogen bonds : angle 5.72269 / 3.97 ( 2643) link_ALPHA1-3 : bond 0.00633 / 0.39 ( 6) link_ALPHA1-3 : angle 1.61802 / 1.16 ( 18) link_ALPHA1-6 : bond 0.00616 / 0.32 ( 1) link_ALPHA1-6 : angle 1.27388 / 0.71 ( 3) link_BETA1-4 : bond 0.00377 / 0.24 ( 33) link_BETA1-4 : angle 1.49166 / 1.06 ( 99) link_NAG-ASN : bond 0.00201 / 0.14 ( 34) link_NAG-ASN : angle 1.60625 / 1.03 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6324 Ramachandran restraints generated. 3162 Oldfield, 0 Emsley, 3162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.976 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 166 ASP cc_start: 0.8744 (m-30) cc_final: 0.8428 (p0) REVERT: A 170 LEU cc_start: 0.4110 (OUTLIER) cc_final: 0.2397 (tp) REVERT: A 417 MET cc_start: 0.2042 (tpt) cc_final: 0.1608 (pmm) REVERT: A 545 PHE cc_start: 0.4044 (OUTLIER) cc_final: 0.3156 (m-10) REVERT: A 738 TYR cc_start: 0.6063 (OUTLIER) cc_final: 0.5585 (m-80) REVERT: A 770 MET cc_start: 0.7933 (mmp) cc_final: 0.7490 (mmm) REVERT: A 952 PHE cc_start: 0.8061 (m-80) cc_final: 0.7844 (m-80) REVERT: A 976 ASP cc_start: 0.7787 (t0) cc_final: 0.7025 (t70) REVERT: A 984 GLN cc_start: 0.8327 (tm-30) cc_final: 0.7753 (tm-30) REVERT: B 56 GLN cc_start: 0.8630 (mp10) cc_final: 0.7757 (pt0) REVERT: B 179 PHE cc_start: 0.6978 (OUTLIER) cc_final: 0.6465 (t80) REVERT: B 515 LEU cc_start: 0.7197 (tp) cc_final: 0.6986 (pp) REVERT: B 916 ILE cc_start: 0.9520 (tp) cc_final: 0.9171 (tt) REVERT: B 1011 MET cc_start: 0.8874 (tpp) cc_final: 0.8251 (tpp) REVERT: B 1013 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7191 (mm-30) REVERT: C 107 MET cc_start: 0.6231 (mmt) cc_final: 0.5937 (mmt) REVERT: C 151 MET cc_start: 0.6029 (mpp) cc_final: 0.4166 (mpp) REVERT: C 217 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8158 (mtmm) REVERT: C 296 ASP cc_start: 0.8130 (m-30) cc_final: 0.7812 (m-30) REVERT: C 329 PHE cc_start: 0.4637 (m-80) cc_final: 0.3982 (m-10) REVERT: C 347 ASN cc_start: 0.8453 (m-40) cc_final: 0.7636 (p0) REVERT: C 600 ASP cc_start: 0.8193 (m-30) cc_final: 0.7646 (m-30) REVERT: C 936 GLN cc_start: 0.8725 (mm110) cc_final: 0.8333 (mm-40) outliers start: 45 outliers final: 35 residues processed: 202 average time/residue: 0.1468 time to fit residues: 50.6927 Evaluate side-chains 203 residues out of total 2779 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 545 PHE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 738 TYR Chi-restraints excluded: chain A residue 772 LYS Chi-restraints excluded: chain A residue 833 CYS Chi-restraints excluded: chain A residue 851 MET Chi-restraints excluded: chain A residue 891 ILE Chi-restraints excluded: chain A residue 1000 ILE Chi-restraints excluded: chain A residue 1052 SER Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain B residue 35 SER Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 705 THR Chi-restraints excluded: chain B residue 840 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 709 MET Chi-restraints excluded: chain C residue 851 MET Chi-restraints excluded: chain C residue 868 TRP Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1059 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 226 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 191 optimal weight: 0.7980 chunk 222 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 292 optimal weight: 3.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 883 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 987 GLN ** C 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1065 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.114820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.088584 restraints weight = 115576.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.088808 restraints weight = 85593.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.088633 restraints weight = 64415.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.089037 restraints weight = 64551.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.089387 restraints weight = 56183.788| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26709 Z= 0.136 Angle : 0.666 15.720 36490 Z= 0.328 Chirality : 0.044 0.210 4303 Planarity : 0.004 0.042 4569 Dihedral : 5.165 33.415 3437 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.69 % Allowed : 13.78 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3162 helix: 0.83 (0.21), residues: 691 sheet: -0.96 (0.20), residues: 651 loop : -1.97 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 126 TYR 0.030 0.001 TYR B 41 PHE 0.038 0.002 PHE B 179 TRP 0.014 0.001 TRP B 423 HIS 0.008 0.001 HIS A1065 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (26590) covalent geometry : angle 0.65349 / 0.32 (36178) SS BOND : bond 0.00354 / 0.19 ( 45) SS BOND : angle 1.71136 / 1.08 ( 90) hydrogen bonds : bond 0.03817 / 2.53 ( 939) hydrogen bonds : angle 5.59146 / 3.89 ( 2643) link_ALPHA1-3 : bond 0.00602 / 0.37 ( 6) link_ALPHA1-3 : angle 1.53294 / 1.09 ( 18) link_ALPHA1-6 : bond 0.00596 / 0.31 ( 1) link_ALPHA1-6 : angle 1.28738 / 0.71 ( 3) link_BETA1-4 : bond 0.00382 / 0.24 ( 33) link_BETA1-4 : angle 1.41495 / 1.00 ( 99) link_NAG-ASN : bond 0.00118 / 0.09 ( 34) link_NAG-ASN : angle 1.48470 / 0.95 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3995.66 seconds wall clock time: 70 minutes 15.17 seconds (4215.17 seconds total)