Starting phenix.real_space_refine on Sun Sep 13 13:37:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6zow_11328/09_2026/6zow_11328.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zow_11328/09_2026/6zow_11328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zow_11328/09_2026/6zow_11328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zow_11328/09_2026/6zow_11328.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6zow_11328/09_2026/6zow_11328.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6zow_11328/09_2026/6zow_11328.cif" model { file = "/net/cci-nas-00/data/ceres_data/6zow_11328/09_2026/6zow_11328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zow_11328/09_2026/6zow_11328.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.029 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 101 5.16 5 C 14930 2.51 5 N 3780 2.21 5 O 4723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23534 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 6212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 6212 Classifications: {'peptide': 801} Link IDs: {'PTRANS': 38, 'TRANS': 762} Chain breaks: 8 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 943, 7367 Classifications: {'peptide': 943} Link IDs: {'PTRANS': 45, 'TRANS': 897} Chain breaks: 12 Chain: "B" Number of atoms: 7243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 930, 7243 Classifications: {'peptide': 930} Link IDs: {'PTRANS': 44, 'TRANS': 885} Chain breaks: 10 Chain: "a" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 10, 'TRANS': 177} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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: 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: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: 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: "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: 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: "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: 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: "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: 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: "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: "Y" 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: "Z" 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: "b" 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: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 81 Unusual residues: {'MAN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 67 Unusual residues: {'MAN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "a" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 30 Unusual residues: {'DMS': 3, 'NAG': 1} Classifications: {'undetermined': 4, 'water': 4} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.91, per 1000 atoms: 0.21 Number of scatterers: 23534 At special positions: 0 Unit cell: (127.734, 130.875, 196.836, 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 101 16.00 O 4723 8.00 N 3780 7.00 C 14930 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS a 336 " - pdb=" SG CYS a 361 " distance=2.03 Simple disulfide: pdb=" SG CYS a 379 " - pdb=" SG CYS a 432 " distance=2.03 Simple disulfide: pdb=" SG CYS a 391 " - pdb=" SG CYS a 525 " distance=2.03 Simple disulfide: pdb=" SG CYS a 480 " - pdb=" SG CYS a 488 " 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=1, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " 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 L 1 " - " NAG L 2 " " 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 2 " - " BMA Q 3 " " 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 U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " BETA1-6 " NAG Q 1 " - " NAG Q 2 " NAG-ASN " NAG A1301 " - " ASN A 603 " " NAG A1302 " - " ASN A 616 " " NAG A1303 " - " ASN A 122 " " NAG A1304 " - " ASN A 165 " " NAG A1305 " - " ASN A 234 " " NAG B1301 " - " ASN B 616 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 331 " " NAG B1305 " - " ASN B 165 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 343 " " NAG C1305 " - " ASN C 165 " " NAG C1306 " - " ASN C 61 " " NAG C1307 " - " ASN C 603 " " NAG C1308 " - " ASN C 122 " " NAG D 1 " - " ASN A 657 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 282 " " NAG K 1 " - " ASN A 331 " " NAG L 1 " - " ASN A 709 " " NAG M 1 " - " ASN C 709 " " NAG N 1 " - " ASN C1134 " " NAG O 1 " - " ASN C1074 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C 801 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 282 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B 717 " " NAG Z 1 " - " ASN B 709 " " NAG a1303 " - " ASN a 343 " " NAG b 1 " - " ASN B 282 " " NAG c 1 " - " ASN B 343 " " NAG d 1 " - " ASN B 122 " " NAG e 1 " - " ASN B 657 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 975.9 milliseconds 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5384 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 44 sheets defined 27.1% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.681A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.713A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.145A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.643A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.749A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.101A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.172A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 344 removed outlier: 3.908A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.139A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.224A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.919A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.502A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.608A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.038A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.572A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.961A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 3.688A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.572A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.127A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.371A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 568 through 572 removed outlier: 3.578A pdb=" N ASP B 571 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR B 572 " --> pdb=" O ILE B 569 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 568 through 572' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.545A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.569A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.626A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.534A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.599A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.244A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.172A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'a' and resid 338 through 343 Processing helix chain 'a' and resid 365 through 370 Processing helix chain 'a' and resid 383 through 387 removed outlier: 3.971A pdb=" N LEU a 387 " --> pdb=" O PRO a 384 " (cutoff:3.500A) Processing helix chain 'a' and resid 404 through 408 removed outlier: 4.384A pdb=" N ARG a 408 " --> pdb=" O GLY a 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 404 through 408' Processing helix chain 'a' and resid 416 through 422 Processing helix chain 'a' and resid 438 through 443 Processing helix chain 'a' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.761A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 51 removed outlier: 3.761A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.445A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.875A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.554A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.414A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.414A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.439A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.142A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 52 removed outlier: 3.765A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 169 through 171 removed outlier: 4.022A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.980A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 326 through 328 removed outlier: 5.273A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 8.300A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AC3, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.334A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.457A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.911A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.911A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AC9, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AD1, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.671A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AD3, first strand: chain 'B' and resid 200 through 207 removed outlier: 3.559A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 119 through 121 Processing sheet with id=AD5, first strand: chain 'B' and resid 309 through 319 removed outlier: 5.728A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.827A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AD8, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.799A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.183A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.560A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.560A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.311A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AE5, first strand: chain 'a' and resid 354 through 358 removed outlier: 4.056A pdb=" N VAL a 395 " --> pdb=" O ILE a 358 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'a' and resid 361 through 362 removed outlier: 6.669A pdb=" N CYS a 361 " --> pdb=" O CYS a 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'a' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'a' and resid 473 through 474 940 hydrogen bonds defined for protein. 2580 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: 4.82 Time building geometry restraints manager: 3.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7309 1.34 - 1.46: 5584 1.46 - 1.58: 10979 1.58 - 1.70: 1 1.70 - 1.82: 128 Bond restraints: 24001 Sorted by residual: bond pdb=" C1 NAG B1302 " pdb=" O5 NAG B1302 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sigma weight residual 1.410 1.475 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " ideal model delta sigma weight residual 1.528 1.588 -0.060 2.00e-02 2.50e+03 9.03e+00 bond pdb=" C5 BMA Q 3 " pdb=" C6 BMA Q 3 " ideal model delta sigma weight residual 1.526 1.470 0.056 2.00e-02 2.50e+03 7.94e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.34e+00 ... (remaining 23996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 31516 1.93 - 3.85: 928 3.85 - 5.78: 148 5.78 - 7.71: 40 7.71 - 9.64: 7 Bond angle restraints: 32639 Sorted by residual: angle pdb=" C ASN B 122 " pdb=" CA ASN B 122 " pdb=" CB ASN B 122 " ideal model delta sigma weight residual 110.16 117.69 -7.53 1.83e+00 2.99e-01 1.69e+01 angle pdb=" C LYS B 854 " pdb=" N PHE B 855 " pdb=" CA PHE B 855 " ideal model delta sigma weight residual 121.90 116.82 5.08 1.26e+00 6.30e-01 1.62e+01 angle pdb=" CA CYS B 738 " pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " ideal model delta sigma weight residual 114.40 123.32 -8.92 2.30e+00 1.89e-01 1.50e+01 angle pdb=" C LEU B 223 " pdb=" N GLU B 224 " pdb=" CA GLU B 224 " ideal model delta sigma weight residual 122.28 118.42 3.86 1.02e+00 9.61e-01 1.43e+01 angle pdb=" C PHE a 347 " pdb=" CA PHE a 347 " pdb=" CB PHE a 347 " ideal model delta sigma weight residual 110.42 117.82 -7.40 1.99e+00 2.53e-01 1.38e+01 ... (remaining 32634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 12337 17.91 - 35.82: 1056 35.82 - 53.74: 182 53.74 - 71.65: 32 71.65 - 89.56: 21 Dihedral angle restraints: 13628 sinusoidal: 5299 harmonic: 8329 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -10.00 -76.00 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -13.30 -72.70 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -154.04 68.04 1 1.00e+01 1.00e-02 6.01e+01 ... (remaining 13625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3810 0.107 - 0.213: 195 0.213 - 0.320: 16 0.320 - 0.427: 1 0.427 - 0.533: 1 Chirality restraints: 4023 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.66e+01 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.11e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 4020 not shown) Planarity restraints: 4122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" O DMS a1301 " -0.204 2.00e-02 2.50e+03 2.78e-01 7.70e+02 pdb=" C1 DMS a1301 " -0.137 2.00e-02 2.50e+03 pdb=" C2 DMS a1301 " -0.137 2.00e-02 2.50e+03 pdb=" S DMS a1301 " 0.478 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O DMS a1302 " 0.201 2.00e-02 2.50e+03 2.75e-01 7.59e+02 pdb=" C1 DMS a1302 " 0.137 2.00e-02 2.50e+03 pdb=" C2 DMS a1302 " 0.137 2.00e-02 2.50e+03 pdb=" S DMS a1302 " -0.475 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O DMS a1304 " 0.173 2.00e-02 2.50e+03 2.41e-01 5.80e+02 pdb=" C1 DMS a1304 " 0.123 2.00e-02 2.50e+03 pdb=" C2 DMS a1304 " 0.120 2.00e-02 2.50e+03 pdb=" S DMS a1304 " -0.416 2.00e-02 2.50e+03 ... (remaining 4119 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 207 2.57 - 3.15: 20121 3.15 - 3.74: 35131 3.74 - 4.32: 49299 4.32 - 4.90: 81218 Nonbonded interactions: 185976 Sorted by model distance: nonbonded pdb=" C LEU A 335 " pdb=" N CYS a 336 " model vdw 1.991 3.350 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.059 3.040 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.087 3.040 nonbonded pdb=" OG1 THR C 553 " pdb=" OD1 ASP C 586 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR C 645 " pdb=" O GLY C 648 " model vdw 2.116 3.040 ... (remaining 185971 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 27 through 66 or resid 82 through 131 or resid 165 through \ 173 or resid 189 through 241 or resid 263 through 620 or resid 641 through 828 \ or resid 854 through 1147 or resid 1302 through 1304)) selection = (chain 'B' and ((resid 27 and (name CA or name C or name O or name CB )) or resi \ d 28 through 131 or resid 165 through 335 or resid 526 through 1303)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'P' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'R' selection = chain 'U' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'W' selection = chain 'Y' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 22.240 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 0.690 24125 Z= 0.535 Angle : 0.856 17.040 32972 Z= 0.414 Chirality : 0.055 0.533 4023 Planarity : 0.008 0.278 4077 Dihedral : 13.619 89.558 8136 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.52 % Allowed : 5.38 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.14), residues: 2792 helix: 0.60 (0.19), residues: 655 sheet: -0.23 (0.20), residues: 623 loop : -1.33 (0.14), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 214 TYR 0.025 0.002 TYR B1067 PHE 0.036 0.002 PHE C 559 TRP 0.022 0.002 TRP B 886 HIS 0.005 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.30 (24001) covalent geometry : angle 0.80220 / 0.40 (32639) SS BOND : bond 0.00513 / 0.30 ( 36) SS BOND : angle 2.00188 / 1.57 ( 72) hydrogen bonds : bond 0.12844 / 8.58 ( 911) hydrogen bonds : angle 7.35048 / 4.90 ( 2580) Misc. bond : bond 0.69018 / 32.87 ( 1) link_ALPHA1-3 : bond 0.00696 / 0.47 ( 4) link_ALPHA1-3 : angle 1.66623 / 1.01 ( 12) link_BETA1-4 : bond 0.00931 / 0.64 ( 37) link_BETA1-4 : angle 3.04655 / 2.09 ( 111) link_BETA1-6 : bond 0.00152 / 0.07 ( 1) link_BETA1-6 : angle 1.69791 / 1.06 ( 3) link_NAG-ASN : bond 0.00631 / 0.43 ( 45) link_NAG-ASN : angle 3.62311 / 2.25 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 268 time to evaluate : 0.874 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: C 1029 MET cc_start: 0.7493 (tpp) cc_final: 0.7284 (tpp) REVERT: a 480 CYS cc_start: 0.4315 (OUTLIER) cc_final: 0.2511 (m) outliers start: 13 outliers final: 6 residues processed: 280 average time/residue: 0.6027 time to fit residues: 195.2594 Evaluate side-chains 150 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 420 ASP Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain a residue 387 LEU Chi-restraints excluded: chain a residue 480 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0030 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 563 GLN A 564 GLN A 644 GLN A 751 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A 901 GLN A 914 ASN A1005 GLN A1010 GLN A1036 GLN A1088 HIS A1106 GLN C 211 ASN C 437 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 784 GLN ** C 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN C1010 GLN C1101 HIS B 125 ASN B 360 ASN B 422 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 ASN B 787 GLN B 913 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1011 GLN B1058 HIS a 501 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.094207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.060052 restraints weight = 67101.900| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 3.89 r_work: 0.2855 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24125 Z= 0.152 Angle : 0.777 16.638 32972 Z= 0.361 Chirality : 0.048 0.299 4023 Planarity : 0.004 0.045 4077 Dihedral : 4.888 57.580 3050 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.83 % Allowed : 12.79 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.15), residues: 2792 helix: 1.44 (0.20), residues: 656 sheet: 0.00 (0.20), residues: 618 loop : -1.28 (0.14), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 319 TYR 0.021 0.001 TYR B1067 PHE 0.031 0.002 PHE C 220 TRP 0.023 0.002 TRP B 64 HIS 0.003 0.001 HIS C 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (24001) covalent geometry : angle 0.74437 / 0.35 (32639) SS BOND : bond 0.00376 / 0.24 ( 36) SS BOND : angle 1.51198 / 1.10 ( 72) hydrogen bonds : bond 0.04707 / 3.11 ( 911) hydrogen bonds : angle 5.87604 / 3.91 ( 2580) Misc. bond : bond 0.00340 / 0.16 ( 1) link_ALPHA1-3 : bond 0.00785 / 0.53 ( 4) link_ALPHA1-3 : angle 1.59758 / 0.96 ( 12) link_BETA1-4 : bond 0.00656 / 0.42 ( 37) link_BETA1-4 : angle 2.36070 / 1.63 ( 111) link_BETA1-6 : bond 0.00295 / 0.14 ( 1) link_BETA1-6 : angle 1.36601 / 0.84 ( 3) link_NAG-ASN : bond 0.00452 / 0.32 ( 45) link_NAG-ASN : angle 2.73086 / 1.73 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 162 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.8685 (t60) cc_final: 0.8340 (t60) REVERT: A 762 GLN cc_start: 0.8945 (mt0) cc_final: 0.8732 (mt0) REVERT: A 990 GLU cc_start: 0.9095 (tt0) cc_final: 0.8660 (mm-30) REVERT: C 269 TYR cc_start: 0.6609 (m-10) cc_final: 0.6251 (m-80) REVERT: B 309 GLU cc_start: 0.8566 (pm20) cc_final: 0.8192 (pm20) REVERT: B 779 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8905 (tm-30) REVERT: B 1050 MET cc_start: 0.9160 (ptp) cc_final: 0.8822 (ptp) outliers start: 46 outliers final: 14 residues processed: 194 average time/residue: 0.5303 time to fit residues: 121.5631 Evaluate side-chains 130 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 896 ILE Chi-restraints excluded: chain a residue 387 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 190 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 195 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 690 GLN A 804 GLN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN A1010 GLN A1011 GLN C 99 ASN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN a 360 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.090031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.056060 restraints weight = 67832.515| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.72 r_work: 0.2750 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.116 24125 Z= 0.429 Angle : 0.891 16.755 32972 Z= 0.422 Chirality : 0.051 0.284 4023 Planarity : 0.005 0.061 4077 Dihedral : 5.043 41.632 3043 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.19 % Allowed : 16.14 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.15), residues: 2792 helix: 1.37 (0.20), residues: 644 sheet: -0.31 (0.19), residues: 665 loop : -1.19 (0.15), residues: 1483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1039 TYR 0.021 0.002 TYR B1067 PHE 0.024 0.002 PHE B 906 TRP 0.020 0.002 TRP B 64 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00983 / 0.43 (24001) covalent geometry : angle 0.85892 / 0.41 (32639) SS BOND : bond 0.00727 / 0.46 ( 36) SS BOND : angle 2.22527 / 1.63 ( 72) hydrogen bonds : bond 0.05309 / 3.52 ( 911) hydrogen bonds : angle 6.08696 / 4.05 ( 2580) Misc. bond : bond 0.00507 / 0.24 ( 1) link_ALPHA1-3 : bond 0.00609 / 0.40 ( 4) link_ALPHA1-3 : angle 1.51515 / 0.93 ( 12) link_BETA1-4 : bond 0.00649 / 0.39 ( 37) link_BETA1-4 : angle 2.36410 / 1.66 ( 111) link_BETA1-6 : bond 0.00266 / 0.13 ( 1) link_BETA1-6 : angle 1.57277 / 1.00 ( 3) link_NAG-ASN : bond 0.00678 / 0.41 ( 45) link_NAG-ASN : angle 2.81546 / 1.86 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 123 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.8705 (m-40) cc_final: 0.8489 (m-40) REVERT: A 780 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8565 (mp0) REVERT: A 990 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8868 (mm-30) REVERT: A 1002 GLN cc_start: 0.9151 (tt0) cc_final: 0.8767 (tp40) REVERT: C 269 TYR cc_start: 0.6762 (m-10) cc_final: 0.6393 (m-10) REVERT: C 298 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: C 360 ASN cc_start: 0.9273 (m110) cc_final: 0.8847 (t0) REVERT: C 417 LYS cc_start: 0.7823 (tmtt) cc_final: 0.7310 (tptt) REVERT: C 869 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8765 (mtt) REVERT: B 515 PHE cc_start: 0.8863 (OUTLIER) cc_final: 0.8273 (p90) REVERT: B 567 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8135 (pmm-80) REVERT: B 1050 MET cc_start: 0.9238 (ptp) cc_final: 0.8907 (ptp) outliers start: 80 outliers final: 30 residues processed: 191 average time/residue: 0.4509 time to fit residues: 103.0635 Evaluate side-chains 144 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain a residue 387 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 31 optimal weight: 1.9990 chunk 179 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 273 optimal weight: 40.0000 chunk 238 optimal weight: 1.9990 chunk 252 optimal weight: 0.5980 chunk 227 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 93 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 177 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 907 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN C 99 ASN C 239 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 613 GLN C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN B 360 ASN B 563 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN B1101 HIS a 450 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.092610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.058260 restraints weight = 67466.400| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.86 r_work: 0.2812 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24125 Z= 0.155 Angle : 0.744 16.673 32972 Z= 0.343 Chirality : 0.047 0.308 4023 Planarity : 0.004 0.042 4077 Dihedral : 4.627 40.125 3042 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.03 % Allowed : 17.05 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.15), residues: 2792 helix: 1.73 (0.20), residues: 650 sheet: -0.23 (0.19), residues: 639 loop : -1.10 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 273 TYR 0.020 0.001 TYR B1067 PHE 0.013 0.001 PHE C 823 TRP 0.017 0.001 TRP C 104 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (24001) covalent geometry : angle 0.71700 / 0.34 (32639) SS BOND : bond 0.00926 / 0.75 ( 36) SS BOND : angle 1.65552 / 1.16 ( 72) hydrogen bonds : bond 0.04255 / 2.83 ( 911) hydrogen bonds : angle 5.58822 / 3.72 ( 2580) Misc. bond : bond 0.00031 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00745 / 0.49 ( 4) link_ALPHA1-3 : angle 1.45399 / 0.88 ( 12) link_BETA1-4 : bond 0.00598 / 0.37 ( 37) link_BETA1-4 : angle 2.08254 / 1.45 ( 111) link_BETA1-6 : bond 0.00611 / 0.29 ( 1) link_BETA1-6 : angle 1.47282 / 0.91 ( 3) link_NAG-ASN : bond 0.00375 / 0.26 ( 45) link_NAG-ASN : angle 2.35612 / 1.52 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 127 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ASN cc_start: 0.8745 (m-40) cc_final: 0.8502 (m-40) REVERT: A 780 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8704 (mm-30) REVERT: A 990 GLU cc_start: 0.9159 (OUTLIER) cc_final: 0.8717 (mm-30) REVERT: A 1002 GLN cc_start: 0.9113 (tt0) cc_final: 0.8626 (tp-100) REVERT: A 1142 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7969 (tp-100) REVERT: C 269 TYR cc_start: 0.6692 (m-10) cc_final: 0.6402 (m-10) REVERT: C 360 ASN cc_start: 0.9268 (m110) cc_final: 0.8835 (t0) REVERT: C 417 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7419 (tptt) REVERT: C 585 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7351 (pp) REVERT: C 748 GLU cc_start: 0.8714 (mp0) cc_final: 0.8479 (pm20) REVERT: C 979 ASP cc_start: 0.8825 (t0) cc_final: 0.8563 (t0) REVERT: B 567 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8122 (pmm-80) REVERT: B 581 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9035 (p) REVERT: B 779 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8783 (tm-30) outliers start: 76 outliers final: 29 residues processed: 188 average time/residue: 0.4756 time to fit residues: 106.4976 Evaluate side-chains 145 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain a residue 387 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 131 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 214 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 246 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 907 ASN A1010 GLN ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.090859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.056806 restraints weight = 67161.598| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.82 r_work: 0.2779 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 24125 Z= 0.302 Angle : 0.795 16.660 32972 Z= 0.370 Chirality : 0.048 0.301 4023 Planarity : 0.004 0.045 4077 Dihedral : 4.631 28.359 3040 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.43 % Allowed : 18.13 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 2792 helix: 1.62 (0.20), residues: 651 sheet: -0.20 (0.19), residues: 645 loop : -1.12 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 273 TYR 0.020 0.001 TYR B1067 PHE 0.020 0.002 PHE B 855 TRP 0.018 0.002 TRP C 104 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.30 (24001) covalent geometry : angle 0.76864 / 0.36 (32639) SS BOND : bond 0.00550 / 0.36 ( 36) SS BOND : angle 1.86553 / 1.46 ( 72) hydrogen bonds : bond 0.04556 / 3.03 ( 911) hydrogen bonds : angle 5.68403 / 3.77 ( 2580) Misc. bond : bond 0.00042 / 0.02 ( 1) link_ALPHA1-3 : bond 0.00598 / 0.40 ( 4) link_ALPHA1-3 : angle 1.49288 / 0.91 ( 12) link_BETA1-4 : bond 0.00588 / 0.36 ( 37) link_BETA1-4 : angle 2.10712 / 1.48 ( 111) link_BETA1-6 : bond 0.00415 / 0.20 ( 1) link_BETA1-6 : angle 1.63633 / 1.02 ( 3) link_NAG-ASN : bond 0.00496 / 0.32 ( 45) link_NAG-ASN : angle 2.38962 / 1.57 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 117 time to evaluate : 0.694 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 776 LYS cc_start: 0.9298 (tppt) cc_final: 0.9011 (ttpt) REVERT: A 990 GLU cc_start: 0.9156 (OUTLIER) cc_final: 0.8759 (mm-30) REVERT: A 1002 GLN cc_start: 0.9134 (tt0) cc_final: 0.8732 (tp40) REVERT: A 1142 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8063 (tp-100) REVERT: C 195 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8191 (pttt) REVERT: C 269 TYR cc_start: 0.6773 (m-10) cc_final: 0.6458 (m-80) REVERT: C 417 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7372 (tptt) REVERT: C 585 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7391 (pp) REVERT: C 748 GLU cc_start: 0.8745 (mp0) cc_final: 0.8521 (pm20) REVERT: C 979 ASP cc_start: 0.8811 (t0) cc_final: 0.8578 (t0) REVERT: B 294 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8723 (t0) REVERT: B 567 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8096 (pmm-80) outliers start: 86 outliers final: 40 residues processed: 190 average time/residue: 0.4746 time to fit residues: 107.1704 Evaluate side-chains 153 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 106 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain a residue 387 LEU Chi-restraints excluded: chain a residue 493 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 5 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 264 optimal weight: 0.4980 chunk 143 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 907 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN C 580 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.092547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058227 restraints weight = 68137.205| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 3.80 r_work: 0.2823 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 24125 Z= 0.151 Angle : 0.737 16.616 32972 Z= 0.340 Chirality : 0.046 0.319 4023 Planarity : 0.004 0.073 4077 Dihedral : 4.408 28.294 3040 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.55 % Allowed : 19.48 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 2792 helix: 1.78 (0.20), residues: 663 sheet: -0.07 (0.20), residues: 624 loop : -1.13 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 214 TYR 0.021 0.001 TYR B1067 PHE 0.016 0.001 PHE B 565 TRP 0.023 0.002 TRP B 64 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (24001) covalent geometry : angle 0.71405 / 0.33 (32639) SS BOND : bond 0.00311 / 0.20 ( 36) SS BOND : angle 1.51237 / 1.09 ( 72) hydrogen bonds : bond 0.04058 / 2.70 ( 911) hydrogen bonds : angle 5.40211 / 3.58 ( 2580) Misc. bond : bond 0.00031 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00756 / 0.51 ( 4) link_ALPHA1-3 : angle 1.46089 / 0.89 ( 12) link_BETA1-4 : bond 0.00568 / 0.36 ( 37) link_BETA1-4 : angle 1.96837 / 1.37 ( 111) link_BETA1-6 : bond 0.00644 / 0.31 ( 1) link_BETA1-6 : angle 1.56298 / 0.97 ( 3) link_NAG-ASN : bond 0.00345 / 0.24 ( 45) link_NAG-ASN : angle 2.14757 / 1.39 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 125 time to evaluate : 0.729 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 87 ASN cc_start: 0.8698 (m-40) cc_final: 0.8435 (m-40) REVERT: A 990 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8759 (mm-30) REVERT: A 1002 GLN cc_start: 0.9079 (tt0) cc_final: 0.8641 (tp-100) REVERT: C 269 TYR cc_start: 0.6736 (m-10) cc_final: 0.6494 (m-80) REVERT: C 360 ASN cc_start: 0.9303 (m-40) cc_final: 0.8841 (t0) REVERT: C 417 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7374 (tptt) REVERT: C 552 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8696 (mm) REVERT: C 585 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7419 (pp) REVERT: C 904 TYR cc_start: 0.8464 (m-10) cc_final: 0.8097 (m-10) REVERT: C 979 ASP cc_start: 0.8740 (t0) cc_final: 0.8480 (t0) REVERT: B 567 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8084 (pmm-80) REVERT: B 1094 VAL cc_start: 0.9320 (OUTLIER) cc_final: 0.9117 (m) outliers start: 64 outliers final: 33 residues processed: 179 average time/residue: 0.4782 time to fit residues: 102.0080 Evaluate side-chains 151 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain a residue 387 LEU Chi-restraints excluded: chain a residue 493 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 122 optimal weight: 9.9990 chunk 273 optimal weight: 30.0000 chunk 87 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 58 optimal weight: 0.6980 chunk 232 optimal weight: 1.9990 chunk 270 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 272 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 762 GLN A 907 ASN A1010 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1005 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.090608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.056731 restraints weight = 67651.142| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.76 r_work: 0.2775 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 24125 Z= 0.316 Angle : 0.792 16.668 32972 Z= 0.369 Chirality : 0.048 0.311 4023 Planarity : 0.004 0.043 4077 Dihedral : 4.530 28.555 3040 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.55 % Allowed : 19.32 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.15), residues: 2792 helix: 1.71 (0.20), residues: 652 sheet: -0.23 (0.20), residues: 625 loop : -1.08 (0.15), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 214 TYR 0.020 0.001 TYR A 904 PHE 0.022 0.002 PHE B 855 TRP 0.022 0.002 TRP C 104 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00729 / 0.32 (24001) covalent geometry : angle 0.76845 / 0.36 (32639) SS BOND : bond 0.00516 / 0.32 ( 36) SS BOND : angle 1.75421 / 1.26 ( 72) hydrogen bonds : bond 0.04426 / 2.94 ( 911) hydrogen bonds : angle 5.54151 / 3.68 ( 2580) Misc. bond : bond 0.00053 / 0.03 ( 1) link_ALPHA1-3 : bond 0.00566 / 0.37 ( 4) link_ALPHA1-3 : angle 1.49579 / 0.91 ( 12) link_BETA1-4 : bond 0.00566 / 0.34 ( 37) link_BETA1-4 : angle 2.03176 / 1.42 ( 111) link_BETA1-6 : bond 0.00419 / 0.20 ( 1) link_BETA1-6 : angle 1.70853 / 1.07 ( 3) link_NAG-ASN : bond 0.00468 / 0.30 ( 45) link_NAG-ASN : angle 2.25337 / 1.49 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 112 time to evaluate : 0.880 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 990 GLU cc_start: 0.9188 (OUTLIER) cc_final: 0.8816 (mm-30) REVERT: A 1002 GLN cc_start: 0.9103 (tt0) cc_final: 0.8726 (tp40) REVERT: A 1142 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8109 (tp-100) REVERT: C 195 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8204 (ptmt) REVERT: C 227 VAL cc_start: 0.8905 (p) cc_final: 0.8612 (t) REVERT: C 269 TYR cc_start: 0.6835 (m-10) cc_final: 0.6529 (m-80) REVERT: C 417 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7362 (tptt) REVERT: C 585 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7326 (pp) REVERT: C 904 TYR cc_start: 0.8470 (m-10) cc_final: 0.8114 (m-10) REVERT: C 979 ASP cc_start: 0.8816 (t0) cc_final: 0.8556 (t0) REVERT: B 294 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8769 (t0) REVERT: B 567 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8100 (pmm-80) REVERT: B 1050 MET cc_start: 0.9332 (ptm) cc_final: 0.9028 (ptp) REVERT: B 1094 VAL cc_start: 0.9348 (OUTLIER) cc_final: 0.9077 (m) outliers start: 89 outliers final: 53 residues processed: 186 average time/residue: 0.4405 time to fit residues: 99.7275 Evaluate side-chains 165 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 104 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 980 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1142 GLN Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain a residue 387 LEU Chi-restraints excluded: chain a residue 493 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 43 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 252 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 218 optimal weight: 0.1980 chunk 214 optimal weight: 0.6980 chunk 168 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 907 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.092554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.058583 restraints weight = 67859.811| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.83 r_work: 0.2836 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24125 Z= 0.141 Angle : 0.733 16.589 32972 Z= 0.337 Chirality : 0.046 0.327 4023 Planarity : 0.004 0.048 4077 Dihedral : 4.327 28.789 3040 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.99 % Allowed : 19.68 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 2792 helix: 1.84 (0.20), residues: 666 sheet: -0.09 (0.20), residues: 633 loop : -1.10 (0.15), residues: 1493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.021 0.001 TYR B1067 PHE 0.012 0.001 PHE C 374 TRP 0.029 0.002 TRP C 104 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (24001) covalent geometry : angle 0.71264 / 0.33 (32639) SS BOND : bond 0.00271 / 0.17 ( 36) SS BOND : angle 1.42669 / 1.00 ( 72) hydrogen bonds : bond 0.03903 / 2.59 ( 911) hydrogen bonds : angle 5.24717 / 3.48 ( 2580) Misc. bond : bond 0.00025 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00687 / 0.45 ( 4) link_ALPHA1-3 : angle 1.45606 / 0.88 ( 12) link_BETA1-4 : bond 0.00594 / 0.37 ( 37) link_BETA1-4 : angle 1.91416 / 1.33 ( 111) link_BETA1-6 : bond 0.00633 / 0.30 ( 1) link_BETA1-6 : angle 1.57529 / 0.97 ( 3) link_NAG-ASN : bond 0.00323 / 0.22 ( 45) link_NAG-ASN : angle 2.02278 / 1.31 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 118 time to evaluate : 0.985 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 87 ASN cc_start: 0.8681 (m-40) cc_final: 0.8413 (m-40) REVERT: A 190 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7517 (mmm160) REVERT: A 990 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8767 (mm-30) REVERT: A 1002 GLN cc_start: 0.9077 (tt0) cc_final: 0.8652 (tp-100) REVERT: C 195 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8112 (pttt) REVERT: C 269 TYR cc_start: 0.6790 (m-10) cc_final: 0.6508 (m-80) REVERT: C 360 ASN cc_start: 0.9267 (m-40) cc_final: 0.8836 (t0) REVERT: C 417 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7469 (tptt) REVERT: C 585 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7353 (pp) REVERT: C 902 MET cc_start: 0.9054 (mmm) cc_final: 0.8854 (tpt) REVERT: C 904 TYR cc_start: 0.8430 (m-10) cc_final: 0.8093 (m-10) REVERT: C 979 ASP cc_start: 0.8717 (t0) cc_final: 0.8452 (t0) REVERT: C 1050 MET cc_start: 0.9135 (ptm) cc_final: 0.8891 (ptm) REVERT: B 200 TYR cc_start: 0.8601 (m-80) cc_final: 0.8299 (t80) REVERT: B 294 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8786 (t0) REVERT: B 567 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8095 (pmm-80) REVERT: B 1002 GLN cc_start: 0.9033 (tt0) cc_final: 0.8806 (tp40) REVERT: B 1094 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.9072 (m) outliers start: 75 outliers final: 43 residues processed: 181 average time/residue: 0.4738 time to fit residues: 102.6334 Evaluate side-chains 162 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain a residue 387 LEU Chi-restraints excluded: chain a residue 493 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 191 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 199 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 262 optimal weight: 0.6980 chunk 29 optimal weight: 0.0270 chunk 65 optimal weight: 0.9990 chunk 280 optimal weight: 40.0000 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 907 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.092910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.059142 restraints weight = 67725.531| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.75 r_work: 0.2846 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24125 Z= 0.128 Angle : 0.720 16.561 32972 Z= 0.330 Chirality : 0.046 0.333 4023 Planarity : 0.004 0.050 4077 Dihedral : 4.220 28.253 3040 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.35 % Allowed : 20.44 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.15), residues: 2792 helix: 1.84 (0.20), residues: 667 sheet: 0.01 (0.20), residues: 620 loop : -1.05 (0.15), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 214 TYR 0.028 0.001 TYR A 904 PHE 0.026 0.001 PHE B 855 TRP 0.031 0.002 TRP C 104 HIS 0.003 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (24001) covalent geometry : angle 0.70025 / 0.32 (32639) SS BOND : bond 0.00263 / 0.17 ( 36) SS BOND : angle 1.38007 / 0.97 ( 72) hydrogen bonds : bond 0.03784 / 2.52 ( 911) hydrogen bonds : angle 5.13415 / 3.41 ( 2580) Misc. bond : bond 0.00024 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00663 / 0.44 ( 4) link_ALPHA1-3 : angle 1.45304 / 0.88 ( 12) link_BETA1-4 : bond 0.00580 / 0.36 ( 37) link_BETA1-4 : angle 1.88734 / 1.32 ( 111) link_BETA1-6 : bond 0.00640 / 0.30 ( 1) link_BETA1-6 : angle 1.57043 / 0.97 ( 3) link_NAG-ASN : bond 0.00302 / 0.21 ( 45) link_NAG-ASN : angle 1.95696 / 1.27 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 117 time to evaluate : 0.922 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 87 ASN cc_start: 0.8664 (m-40) cc_final: 0.8389 (m-40) REVERT: A 780 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8455 (mp0) REVERT: A 990 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8812 (mm-30) REVERT: A 1002 GLN cc_start: 0.9057 (tt0) cc_final: 0.8642 (tp-100) REVERT: C 195 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8028 (pttt) REVERT: C 269 TYR cc_start: 0.6748 (m-10) cc_final: 0.6479 (m-80) REVERT: C 360 ASN cc_start: 0.9276 (m-40) cc_final: 0.8836 (t0) REVERT: C 417 LYS cc_start: 0.7827 (OUTLIER) cc_final: 0.7488 (tptt) REVERT: C 585 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7319 (pp) REVERT: C 731 MET cc_start: 0.8951 (ttm) cc_final: 0.8666 (mtp) REVERT: C 979 ASP cc_start: 0.8727 (t0) cc_final: 0.8474 (t0) REVERT: B 200 TYR cc_start: 0.8593 (m-80) cc_final: 0.8335 (t80) REVERT: B 294 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8786 (t0) REVERT: B 567 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8099 (pmm-80) REVERT: B 1002 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8822 (tp40) REVERT: B 1050 MET cc_start: 0.9339 (ptm) cc_final: 0.8986 (ptp) outliers start: 59 outliers final: 39 residues processed: 165 average time/residue: 0.4703 time to fit residues: 92.9760 Evaluate side-chains 158 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 112 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1005 GLN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain a residue 387 LEU Chi-restraints excluded: chain a residue 493 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 144 optimal weight: 0.0030 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 86 optimal weight: 0.7980 chunk 255 optimal weight: 0.5980 chunk 239 optimal weight: 2.9990 chunk 258 optimal weight: 0.9980 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 907 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1005 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN B1002 GLN B1005 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.092931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.059231 restraints weight = 68018.785| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 3.78 r_work: 0.2848 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24125 Z= 0.138 Angle : 0.737 18.797 32972 Z= 0.339 Chirality : 0.046 0.334 4023 Planarity : 0.004 0.048 4077 Dihedral : 4.214 30.070 3040 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.27 % Allowed : 20.76 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.12 (0.15), residues: 2792 helix: 1.86 (0.20), residues: 666 sheet: 0.00 (0.20), residues: 601 loop : -1.01 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 214 TYR 0.022 0.001 TYR A 904 PHE 0.017 0.001 PHE B 377 TRP 0.030 0.002 TRP C 104 HIS 0.003 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (24001) covalent geometry : angle 0.70997 / 0.33 (32639) SS BOND : bond 0.00273 / 0.17 ( 36) SS BOND : angle 2.72009 / 1.73 ( 72) hydrogen bonds : bond 0.03764 / 2.51 ( 911) hydrogen bonds : angle 5.09763 / 3.37 ( 2580) Misc. bond : bond 0.00024 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00640 / 0.41 ( 4) link_ALPHA1-3 : angle 1.45716 / 0.88 ( 12) link_BETA1-4 : bond 0.00576 / 0.36 ( 37) link_BETA1-4 : angle 1.87489 / 1.31 ( 111) link_BETA1-6 : bond 0.00628 / 0.30 ( 1) link_BETA1-6 : angle 1.57333 / 0.97 ( 3) link_NAG-ASN : bond 0.00296 / 0.20 ( 45) link_NAG-ASN : angle 1.91123 / 1.24 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5584 Ramachandran restraints generated. 2792 Oldfield, 0 Emsley, 2792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 117 time to evaluate : 0.911 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 87 ASN cc_start: 0.8662 (m-40) cc_final: 0.8385 (m-40) REVERT: A 780 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8448 (mp0) REVERT: A 990 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8805 (mm-30) REVERT: A 1002 GLN cc_start: 0.9068 (tt0) cc_final: 0.8649 (tp-100) REVERT: C 195 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8043 (pttt) REVERT: C 269 TYR cc_start: 0.6775 (m-10) cc_final: 0.6513 (m-80) REVERT: C 360 ASN cc_start: 0.9285 (m-40) cc_final: 0.8840 (t0) REVERT: C 417 LYS cc_start: 0.7878 (OUTLIER) cc_final: 0.7565 (tptt) REVERT: C 731 MET cc_start: 0.8942 (ttm) cc_final: 0.8581 (mtp) REVERT: C 979 ASP cc_start: 0.8726 (t0) cc_final: 0.8476 (t0) REVERT: B 200 TYR cc_start: 0.8673 (m-80) cc_final: 0.8422 (t80) REVERT: B 294 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8784 (t0) REVERT: B 567 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8111 (pmm-80) REVERT: B 731 MET cc_start: 0.9147 (ptm) cc_final: 0.8923 (ptt) REVERT: B 1002 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8732 (tp40) REVERT: B 1050 MET cc_start: 0.9323 (ptm) cc_final: 0.8943 (ptp) REVERT: a 501 ASN cc_start: 0.7292 (m110) cc_final: 0.6939 (p0) outliers start: 57 outliers final: 45 residues processed: 166 average time/residue: 0.4604 time to fit residues: 91.3003 Evaluate side-chains 162 residues out of total 2510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 111 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1116 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 417 LYS Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 866 THR Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 974 SER Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 662 CYS Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 828 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain a residue 387 LEU Chi-restraints excluded: chain a residue 493 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 0.6980 chunk 245 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 143 optimal weight: 0.9990 chunk 270 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 907 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN A1010 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.092904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.059211 restraints weight = 67907.921| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.78 r_work: 0.2846 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 24125 Z= 0.207 Angle : 0.972 59.197 32972 Z= 0.498 Chirality : 0.051 1.252 4023 Planarity : 0.005 0.121 4077 Dihedral : 4.312 43.689 3040 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.62 % Favored : 96.31 % Rotamer: Outliers : 2.19 % Allowed : 20.84 % Favored : 76.97 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.14 (0.15), residues: 2792 helix: 1.81 (0.20), residues: 666 sheet: 0.01 (0.20), residues: 601 loop : -1.02 (0.15), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 214 TYR 0.022 0.001 TYR C 904 PHE 0.016 0.001 PHE B 565 TRP 0.027 0.002 TRP C 104 HIS 0.003 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.21 (24001) covalent geometry : angle 0.95520 / 0.49 (32639) SS BOND : bond 0.00330 / 0.21 ( 36) SS BOND : angle 2.48993 / 1.59 ( 72) hydrogen bonds : bond 0.03777 / 2.52 ( 911) hydrogen bonds : angle 5.10398 / 3.38 ( 2580) Misc. bond : bond 0.00026 / 0.01 ( 1) link_ALPHA1-3 : bond 0.00653 / 0.42 ( 4) link_ALPHA1-3 : angle 1.47039 / 0.89 ( 12) link_BETA1-4 : bond 0.00575 / 0.36 ( 37) link_BETA1-4 : angle 1.87980 / 1.31 ( 111) link_BETA1-6 : bond 0.00608 / 0.29 ( 1) link_BETA1-6 : angle 1.59873 / 0.99 ( 3) link_NAG-ASN : bond 0.00294 / 0.20 ( 45) link_NAG-ASN : angle 1.90999 / 1.24 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6299.35 seconds wall clock time: 108 minutes 39.14 seconds (6519.14 seconds total)