Starting phenix.real_space_refine on Fri Mar 6 23:47:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kml_22926/03_2026/7kml_22926.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kml_22926/03_2026/7kml_22926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kml_22926/03_2026/7kml_22926.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kml_22926/03_2026/7kml_22926.map" model { file = "/net/cci-nas-00/data/ceres_data/7kml_22926/03_2026/7kml_22926.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kml_22926/03_2026/7kml_22926.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.065 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 156 5.16 5 C 22239 2.51 5 N 5757 2.21 5 O 6984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 207 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35136 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8078 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 55, 'TRANS': 978} Chain breaks: 7 Chain: "B" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8078 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 55, 'TRANS': 978} Chain breaks: 7 Chain: "C" Number of atoms: 8078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8078 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 55, 'TRANS': 978} Chain breaks: 7 Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "H" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "M" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "I" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "N" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1641 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "J" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1635 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 7.84, per 1000 atoms: 0.22 Number of scatterers: 35136 At special positions: 0 Unit cell: (147.29, 148.32, 224.54, 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 156 16.00 O 6984 8.00 N 5757 7.00 C 22239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.08 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.22 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.08 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.07 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.08 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.22 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.08 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.07 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=2.02 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.08 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.22 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.08 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.07 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 154 " - pdb=" SG CYS L 214 " distance=2.03 Simple disulfide: pdb=" SG CYS L 234 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 104 " distance=2.02 Simple disulfide: pdb=" SG CYS M 154 " - pdb=" SG CYS M 214 " distance=2.03 Simple disulfide: pdb=" SG CYS M 234 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 104 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 211 " distance=2.04 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 104 " distance=2.03 Simple disulfide: pdb=" SG CYS N 154 " - pdb=" SG CYS N 214 " distance=2.03 Simple disulfide: pdb=" SG CYS N 234 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 104 " distance=2.03 Simple disulfide: pdb=" SG CYS J 155 " - pdb=" SG CYS J 211 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A1134 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 165 " " NAG B1303 " - " ASN B 234 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B1134 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 165 " " NAG C1303 " - " ASN C 234 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C1134 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG K 1 " - " ASN A 709 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A1074 " " NAG R 1 " - " ASN A1098 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 282 " " NAG U 1 " - " ASN B 331 " " NAG V 1 " - " ASN B 343 " " NAG W 1 " - " ASN B 709 " " NAG X 1 " - " ASN B 717 " " NAG Y 1 " - " ASN B 801 " " NAG Z 1 " - " ASN B1074 " " NAG a 1 " - " ASN B1098 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 282 " " NAG d 1 " - " ASN C 331 " " NAG e 1 " - " ASN C 343 " " NAG f 1 " - " ASN C 709 " " NAG g 1 " - " ASN C 717 " " NAG h 1 " - " ASN C 801 " " NAG i 1 " - " ASN C1074 " " NAG j 1 " - " ASN C1098 " Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.4 seconds 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8208 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 78 sheets defined 20.0% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 366 through 372 removed outlier: 3.774A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 757 Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.675A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 967 removed outlier: 4.172A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.716A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 366 through 372 removed outlier: 3.775A pdb=" N ALA B 372 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 439 through 441 No H-bonds generated for 'chain 'B' and resid 439 through 441' Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 757 Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.675A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 885 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 967 removed outlier: 4.172A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.716A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 366 through 372 removed outlier: 3.775A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 439 through 441 No H-bonds generated for 'chain 'C' and resid 439 through 441' Processing helix chain 'C' and resid 569 through 571 No H-bonds generated for 'chain 'C' and resid 569 through 571' Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.675A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 885 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 967 removed outlier: 4.172A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.716A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 143 through 147 Processing helix chain 'L' and resid 203 through 207 Processing helix chain 'H' and resid 69 through 72 Processing helix chain 'H' and resid 95 through 99 Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 202 through 206 Processing helix chain 'H' and resid 216 through 219 Processing helix chain 'M' and resid 95 through 99 Processing helix chain 'M' and resid 143 through 147 Processing helix chain 'M' and resid 203 through 207 Processing helix chain 'I' and resid 69 through 72 Processing helix chain 'I' and resid 95 through 99 Processing helix chain 'I' and resid 171 through 173 No H-bonds generated for 'chain 'I' and resid 171 through 173' Processing helix chain 'I' and resid 202 through 206 Processing helix chain 'I' and resid 216 through 219 Processing helix chain 'N' and resid 95 through 99 Processing helix chain 'N' and resid 143 through 147 Processing helix chain 'N' and resid 203 through 207 Processing helix chain 'J' and resid 69 through 72 Processing helix chain 'J' and resid 95 through 99 Processing helix chain 'J' and resid 171 through 173 No H-bonds generated for 'chain 'J' and resid 171 through 173' Processing helix chain 'J' and resid 202 through 206 Processing helix chain 'J' and resid 216 through 219 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.336A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 7.491A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.034A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 11.438A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.479A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.863A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ARG A 403 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.411A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 448 through 454 removed outlier: 7.471A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR A 495 " --> pdb=" O TYR A 451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 6.705A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 703 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.653A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.125A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 789 removed outlier: 6.241A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.602A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.336A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.605A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.491A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.034A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 11.438A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 10.127A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.478A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.863A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.411A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 448 through 454 removed outlier: 7.471A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR B 495 " --> pdb=" O TYR B 451 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.705A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.653A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.125A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 787 through 789 removed outlier: 6.241A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.602A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.336A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.604A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 7.491A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.034A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 11.438A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.128A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.395A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.479A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.863A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 348 through 349 removed outlier: 6.945A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.325A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.411A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 448 through 454 removed outlier: 7.471A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR C 495 " --> pdb=" O TYR C 451 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.705A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.652A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.125A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.602A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.543A pdb=" N LEU L 11 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR L 55 " --> pdb=" O VAL L 39 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.543A pdb=" N LEU L 11 " --> pdb=" O GLU L 125 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 134 through 138 removed outlier: 5.427A pdb=" N TYR L 193 " --> pdb=" O ASN L 158 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 173 through 174 Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 11 through 13 removed outlier: 7.217A pdb=" N TYR H 37 " --> pdb=" O TYR H 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR H 57 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET H 39 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP H 41 " --> pdb=" O VAL H 53 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 166 through 169 Processing sheet with id=AG5, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AG6, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.543A pdb=" N LEU M 11 " --> pdb=" O GLU M 125 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL M 39 " --> pdb=" O TYR M 55 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N TYR M 55 " --> pdb=" O VAL M 39 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.543A pdb=" N LEU M 11 " --> pdb=" O GLU M 125 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 134 through 138 removed outlier: 5.427A pdb=" N TYR M 193 " --> pdb=" O ASN M 158 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'M' and resid 173 through 174 Processing sheet with id=AH1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AH2, first strand: chain 'I' and resid 11 through 13 removed outlier: 7.217A pdb=" N TYR I 37 " --> pdb=" O TYR I 57 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR I 57 " --> pdb=" O TYR I 37 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N MET I 39 " --> pdb=" O GLY I 55 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY I 55 " --> pdb=" O MET I 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP I 41 " --> pdb=" O VAL I 53 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR I 191 " --> pdb=" O ASP I 159 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'I' and resid 166 through 169 Processing sheet with id=AH6, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AH7, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.542A pdb=" N LEU N 11 " --> pdb=" O GLU N 125 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL N 39 " --> pdb=" O TYR N 55 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR N 55 " --> pdb=" O VAL N 39 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP N 41 " --> pdb=" O LEU N 53 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.542A pdb=" N LEU N 11 " --> pdb=" O GLU N 125 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'N' and resid 134 through 138 removed outlier: 5.427A pdb=" N TYR N 193 " --> pdb=" O ASN N 158 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'N' and resid 173 through 174 Processing sheet with id=AI2, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AI3, first strand: chain 'J' and resid 11 through 13 removed outlier: 7.217A pdb=" N TYR J 37 " --> pdb=" O TYR J 57 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N TYR J 57 " --> pdb=" O TYR J 37 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N MET J 39 " --> pdb=" O GLY J 55 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY J 55 " --> pdb=" O MET J 39 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TRP J 41 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR J 191 " --> pdb=" O ASP J 159 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 135 through 139 removed outlier: 5.524A pdb=" N TYR J 191 " --> pdb=" O ASP J 159 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 166 through 169 1481 hydrogen bonds defined for protein. 3897 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: 9.70 Time building geometry restraints manager: 4.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 7113 1.32 - 1.47: 12747 1.47 - 1.61: 15822 1.61 - 1.75: 48 1.75 - 1.89: 186 Bond restraints: 35916 Sorted by residual: bond pdb=" NE ARG B 78 " pdb=" CZ ARG B 78 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.54e+01 bond pdb=" NE ARG C 78 " pdb=" CZ ARG C 78 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.50e+01 bond pdb=" NE ARG A 78 " pdb=" CZ ARG A 78 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.50e+01 bond pdb=" CB HIS H 215 " pdb=" CG HIS H 215 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.05e+01 bond pdb=" CB HIS J 215 " pdb=" CG HIS J 215 " ideal model delta sigma weight residual 1.497 1.408 0.089 1.40e-02 5.10e+03 4.04e+01 ... (remaining 35911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 41004 2.40 - 4.80: 6513 4.80 - 7.20: 1160 7.20 - 9.60: 161 9.60 - 12.00: 29 Bond angle restraints: 48867 Sorted by residual: angle pdb=" N LYS A 97 " pdb=" CA LYS A 97 " pdb=" C LYS A 97 " ideal model delta sigma weight residual 114.04 102.04 12.00 1.24e+00 6.50e-01 9.37e+01 angle pdb=" N LYS C 97 " pdb=" CA LYS C 97 " pdb=" C LYS C 97 " ideal model delta sigma weight residual 114.04 102.04 12.00 1.24e+00 6.50e-01 9.36e+01 angle pdb=" N LYS B 97 " pdb=" CA LYS B 97 " pdb=" C LYS B 97 " ideal model delta sigma weight residual 114.04 102.06 11.98 1.24e+00 6.50e-01 9.34e+01 angle pdb=" C CYS A 336 " pdb=" N PRO A 337 " pdb=" CA PRO A 337 " ideal model delta sigma weight residual 119.82 128.42 -8.60 9.80e-01 1.04e+00 7.71e+01 angle pdb=" C CYS C 336 " pdb=" N PRO C 337 " pdb=" CA PRO C 337 " ideal model delta sigma weight residual 119.82 128.41 -8.59 9.80e-01 1.04e+00 7.69e+01 ... (remaining 48862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.26: 21637 21.26 - 42.52: 527 42.52 - 63.78: 162 63.78 - 85.04: 87 85.04 - 106.30: 39 Dihedral angle restraints: 22452 sinusoidal: 9660 harmonic: 12792 Sorted by residual: dihedral pdb=" CB CYS C 743 " pdb=" SG CYS C 743 " pdb=" SG CYS C 749 " pdb=" CB CYS C 749 " ideal model delta sinusoidal sigma weight residual 93.00 -177.09 -89.91 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS B 743 " pdb=" SG CYS B 743 " pdb=" SG CYS B 749 " pdb=" CB CYS B 749 " ideal model delta sinusoidal sigma weight residual 93.00 -177.10 -89.90 1 1.00e+01 1.00e-02 9.58e+01 dihedral pdb=" CB CYS A 743 " pdb=" SG CYS A 743 " pdb=" SG CYS A 749 " pdb=" CB CYS A 749 " ideal model delta sinusoidal sigma weight residual 93.00 -177.11 -89.89 1 1.00e+01 1.00e-02 9.58e+01 ... (remaining 22449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4375 0.110 - 0.219: 1202 0.219 - 0.329: 171 0.329 - 0.438: 11 0.438 - 0.548: 7 Chirality restraints: 5766 Sorted by residual: chirality pdb=" C1 NAG a 2 " pdb=" O4 NAG a 1 " pdb=" C2 NAG a 2 " pdb=" O5 NAG a 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.76e+01 chirality pdb=" C1 NAG j 2 " pdb=" O4 NAG j 1 " pdb=" C2 NAG j 2 " pdb=" O5 NAG j 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.64e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.53e+01 ... (remaining 5763 not shown) Planarity restraints: 6249 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 42 " 0.073 2.00e-02 2.50e+03 4.11e-02 3.38e+01 pdb=" CG TYR L 42 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR L 42 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR L 42 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR L 42 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR L 42 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR L 42 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR L 42 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 42 " 0.073 2.00e-02 2.50e+03 4.11e-02 3.37e+01 pdb=" CG TYR M 42 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR M 42 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR M 42 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR M 42 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR M 42 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR M 42 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR M 42 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 42 " 0.073 2.00e-02 2.50e+03 4.11e-02 3.37e+01 pdb=" CG TYR N 42 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR N 42 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 TYR N 42 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR N 42 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR N 42 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR N 42 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR N 42 " 0.065 2.00e-02 2.50e+03 ... (remaining 6246 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.91: 14504 2.91 - 3.41: 31878 3.41 - 3.91: 61921 3.91 - 4.40: 70570 4.40 - 4.90: 112736 Nonbonded interactions: 291609 Sorted by model distance: nonbonded pdb=" C4 NAG h 1 " pdb=" O5 NAG h 2 " model vdw 2.415 2.776 nonbonded pdb=" C4 NAG P 1 " pdb=" O5 NAG P 2 " model vdw 2.415 2.776 nonbonded pdb=" C4 NAG Y 1 " pdb=" O5 NAG Y 2 " model vdw 2.415 2.776 nonbonded pdb=" NZ LYS J 221 " pdb=" OD2 ASP J 223 " model vdw 2.416 3.120 nonbonded pdb=" NZ LYS I 221 " pdb=" OD2 ASP I 223 " model vdw 2.416 3.120 ... (remaining 291604 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'U' selection = chain 'V' selection = chain 'd' selection = chain 'e' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.380 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: 0.520 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 34.500 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 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 : 0.018 0.188 36051 Z= 0.941 Angle : 1.879 12.002 49215 Z= 1.264 Chirality : 0.099 0.548 5766 Planarity : 0.009 0.042 6204 Dihedral : 12.304 106.302 14073 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 0.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.39 % Allowed : 0.76 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.45 (0.12), residues: 4353 helix: -0.37 (0.17), residues: 690 sheet: 0.74 (0.14), residues: 1269 loop : 0.40 (0.13), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1000 TYR 0.074 0.011 TYR B 204 PHE 0.039 0.007 PHE B 140 TRP 0.067 0.013 TRP A 353 HIS 0.009 0.002 HIS L 108 Details of bonding type rmsd covalent geometry : bond 0.01798 (35916) covalent geometry : angle 1.87487 (48867) SS BOND : bond 0.04722 ( 57) SS BOND : angle 3.04255 ( 114) hydrogen bonds : bond 0.18008 ( 1430) hydrogen bonds : angle 8.80310 ( 3897) link_BETA1-4 : bond 0.00348 ( 33) link_BETA1-4 : angle 1.36828 ( 99) link_NAG-ASN : bond 0.00436 ( 45) link_NAG-ASN : angle 2.34110 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 667 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 PHE cc_start: 0.9546 (m-10) cc_final: 0.8998 (m-80) REVERT: A 369 TYR cc_start: 0.9016 (t80) cc_final: 0.8729 (t80) REVERT: A 727 LEU cc_start: 0.9356 (mp) cc_final: 0.9081 (mt) REVERT: A 759 PHE cc_start: 0.8526 (t80) cc_final: 0.7968 (t80) REVERT: A 763 LEU cc_start: 0.9549 (mt) cc_final: 0.8941 (mp) REVERT: A 781 VAL cc_start: 0.9559 (t) cc_final: 0.9282 (m) REVERT: A 826 VAL cc_start: 0.8347 (t) cc_final: 0.8125 (t) REVERT: A 878 LEU cc_start: 0.9490 (mt) cc_final: 0.9264 (mt) REVERT: A 886 TRP cc_start: 0.6804 (p-90) cc_final: 0.6521 (p-90) REVERT: A 919 ASN cc_start: 0.8948 (m-40) cc_final: 0.8538 (t0) REVERT: A 936 ASP cc_start: 0.9241 (m-30) cc_final: 0.8678 (t0) REVERT: A 1014 ARG cc_start: 0.9056 (mtt180) cc_final: 0.8662 (ttm170) REVERT: A 1021 SER cc_start: 0.9672 (m) cc_final: 0.9093 (t) REVERT: A 1052 PHE cc_start: 0.9070 (m-80) cc_final: 0.8768 (m-10) REVERT: A 1125 ASN cc_start: 0.7713 (t0) cc_final: 0.7491 (t0) REVERT: B 175 PHE cc_start: 0.9515 (m-10) cc_final: 0.8978 (m-80) REVERT: B 318 PHE cc_start: 0.8339 (t80) cc_final: 0.8074 (t80) REVERT: B 369 TYR cc_start: 0.9057 (t80) cc_final: 0.8797 (t80) REVERT: B 610 VAL cc_start: 0.9387 (t) cc_final: 0.9098 (p) REVERT: B 727 LEU cc_start: 0.9388 (mp) cc_final: 0.8893 (mt) REVERT: B 759 PHE cc_start: 0.8612 (t80) cc_final: 0.7825 (t80) REVERT: B 763 LEU cc_start: 0.9598 (mt) cc_final: 0.8984 (mp) REVERT: B 781 VAL cc_start: 0.9512 (t) cc_final: 0.9230 (m) REVERT: B 878 LEU cc_start: 0.9513 (mt) cc_final: 0.9250 (mt) REVERT: B 886 TRP cc_start: 0.6832 (p-90) cc_final: 0.6398 (p-90) REVERT: B 919 ASN cc_start: 0.8906 (m-40) cc_final: 0.8519 (t0) REVERT: B 936 ASP cc_start: 0.9228 (m-30) cc_final: 0.8691 (t0) REVERT: B 1014 ARG cc_start: 0.9038 (mtt180) cc_final: 0.8741 (mtm-85) REVERT: B 1040 VAL cc_start: 0.8769 (t) cc_final: 0.8536 (t) REVERT: B 1125 ASN cc_start: 0.7746 (t0) cc_final: 0.7526 (t0) REVERT: C 175 PHE cc_start: 0.9566 (m-10) cc_final: 0.9175 (m-80) REVERT: C 318 PHE cc_start: 0.8307 (t80) cc_final: 0.8005 (t80) REVERT: C 369 TYR cc_start: 0.9055 (t80) cc_final: 0.8801 (t80) REVERT: C 610 VAL cc_start: 0.9336 (t) cc_final: 0.9025 (p) REVERT: C 727 LEU cc_start: 0.9353 (mp) cc_final: 0.8847 (mt) REVERT: C 759 PHE cc_start: 0.8527 (t80) cc_final: 0.7577 (t80) REVERT: C 763 LEU cc_start: 0.9632 (mt) cc_final: 0.9008 (mp) REVERT: C 780 GLU cc_start: 0.8830 (tp30) cc_final: 0.8503 (tp30) REVERT: C 781 VAL cc_start: 0.9501 (t) cc_final: 0.9231 (m) REVERT: C 826 VAL cc_start: 0.8091 (t) cc_final: 0.7841 (t) REVERT: C 919 ASN cc_start: 0.8846 (m-40) cc_final: 0.8481 (t0) REVERT: C 922 LEU cc_start: 0.9475 (mp) cc_final: 0.9267 (mm) REVERT: C 936 ASP cc_start: 0.9213 (m-30) cc_final: 0.8689 (t0) REVERT: C 1014 ARG cc_start: 0.9082 (mtt180) cc_final: 0.8869 (ttm170) REVERT: C 1021 SER cc_start: 0.9670 (m) cc_final: 0.9083 (t) REVERT: C 1031 GLU cc_start: 0.8367 (mm-30) cc_final: 0.7985 (mt-10) REVERT: C 1125 ASN cc_start: 0.7675 (t0) cc_final: 0.7454 (t0) REVERT: L 4 MET cc_start: 0.7687 (mmm) cc_final: 0.4264 (tpp) REVERT: H 39 MET cc_start: 0.5272 (mmp) cc_final: 0.4908 (mpp) REVERT: M 4 MET cc_start: 0.7317 (mmm) cc_final: 0.3736 (tpp) REVERT: I 39 MET cc_start: 0.5240 (mmp) cc_final: 0.4889 (mpp) REVERT: N 4 MET cc_start: 0.7524 (mmm) cc_final: 0.4431 (tpp) outliers start: 15 outliers final: 10 residues processed: 682 average time/residue: 0.2471 time to fit residues: 259.1858 Evaluate side-chains 335 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 325 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain C residue 562 PHE Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 1074 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 5.9990 chunk 424 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 439 ASN A 501 ASN A 544 ASN A 901 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 ASN B 544 ASN B 762 GLN B 965 GLN C 49 HIS C 501 ASN C 544 ASN C 690 GLN C 762 GLN C 901 GLN C 907 ASN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN I 186 GLN J 186 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.063930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.052479 restraints weight = 353904.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.053751 restraints weight = 179918.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.054524 restraints weight = 111279.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.054971 restraints weight = 79550.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.055299 restraints weight = 63796.580| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 36051 Z= 0.246 Angle : 0.850 16.553 49215 Z= 0.441 Chirality : 0.049 0.355 5766 Planarity : 0.005 0.042 6204 Dihedral : 8.707 62.247 6374 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.94 % Allowed : 6.73 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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 (0.12), residues: 4353 helix: 0.99 (0.19), residues: 678 sheet: 0.33 (0.14), residues: 1299 loop : 0.09 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1039 TYR 0.031 0.003 TYR C1110 PHE 0.027 0.003 PHE B 377 TRP 0.024 0.003 TRP A 152 HIS 0.010 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00532 (35916) covalent geometry : angle 0.82210 (48867) SS BOND : bond 0.00450 ( 57) SS BOND : angle 1.28090 ( 114) hydrogen bonds : bond 0.05929 ( 1430) hydrogen bonds : angle 7.28064 ( 3897) link_BETA1-4 : bond 0.00683 ( 33) link_BETA1-4 : angle 2.02136 ( 99) link_NAG-ASN : bond 0.00447 ( 45) link_NAG-ASN : angle 3.75513 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 353 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 34 ARG cc_start: 0.6980 (mmm-85) cc_final: 0.6677 (mmm-85) REVERT: A 513 LEU cc_start: 0.8864 (tp) cc_final: 0.8548 (pp) REVERT: A 740 MET cc_start: 0.8481 (mmt) cc_final: 0.7931 (mmt) REVERT: A 902 MET cc_start: 0.9370 (mmm) cc_final: 0.9004 (tpp) REVERT: A 916 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8248 (pp) REVERT: A 936 ASP cc_start: 0.9070 (m-30) cc_final: 0.8684 (t0) REVERT: A 1002 GLN cc_start: 0.8766 (tm-30) cc_final: 0.8186 (tm-30) REVERT: A 1021 SER cc_start: 0.9693 (m) cc_final: 0.9185 (t) REVERT: A 1029 MET cc_start: 0.7471 (tmm) cc_final: 0.6904 (tmm) REVERT: A 1047 TYR cc_start: 0.4246 (OUTLIER) cc_final: 0.3096 (m-80) REVERT: A 1123 SER cc_start: 0.7819 (t) cc_final: 0.7485 (t) REVERT: A 1125 ASN cc_start: 0.8049 (t0) cc_final: 0.7823 (t0) REVERT: B 513 LEU cc_start: 0.8860 (tp) cc_final: 0.8562 (pp) REVERT: B 775 ASP cc_start: 0.8937 (m-30) cc_final: 0.8649 (m-30) REVERT: B 776 LYS cc_start: 0.9505 (tmtt) cc_final: 0.9288 (tptp) REVERT: B 780 GLU cc_start: 0.9209 (tp30) cc_final: 0.8800 (tp30) REVERT: B 796 ASP cc_start: 0.8859 (m-30) cc_final: 0.8622 (p0) REVERT: B 902 MET cc_start: 0.9043 (tpp) cc_final: 0.8455 (tpp) REVERT: B 916 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8199 (pp) REVERT: B 936 ASP cc_start: 0.9123 (m-30) cc_final: 0.8741 (t0) REVERT: B 1001 LEU cc_start: 0.9743 (OUTLIER) cc_final: 0.9421 (pp) REVERT: B 1052 PHE cc_start: 0.9360 (m-10) cc_final: 0.9052 (m-10) REVERT: B 1123 SER cc_start: 0.7835 (t) cc_final: 0.7492 (t) REVERT: B 1125 ASN cc_start: 0.8029 (t0) cc_final: 0.7796 (t0) REVERT: C 513 LEU cc_start: 0.8969 (tp) cc_final: 0.8598 (pp) REVERT: C 796 ASP cc_start: 0.8860 (m-30) cc_final: 0.8573 (p0) REVERT: C 869 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8868 (ptp) REVERT: C 902 MET cc_start: 0.9299 (mmm) cc_final: 0.8837 (mmm) REVERT: C 936 ASP cc_start: 0.9077 (m-30) cc_final: 0.8679 (t0) REVERT: C 1002 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8081 (tm-30) REVERT: C 1017 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8758 (pp20) REVERT: C 1021 SER cc_start: 0.9641 (m) cc_final: 0.9318 (p) REVERT: C 1029 MET cc_start: 0.7538 (tmm) cc_final: 0.7038 (tmm) REVERT: C 1123 SER cc_start: 0.7895 (t) cc_final: 0.7588 (t) REVERT: C 1125 ASN cc_start: 0.7936 (t0) cc_final: 0.7688 (t0) REVERT: L 1 ASP cc_start: 0.8028 (m-30) cc_final: 0.7750 (t0) REVERT: L 4 MET cc_start: 0.5308 (mmm) cc_final: 0.4155 (tpp) REVERT: L 162 ARG cc_start: 0.8971 (tpt90) cc_final: 0.8381 (tpp80) REVERT: M 4 MET cc_start: 0.5204 (mmm) cc_final: 0.3815 (tpp) REVERT: M 162 ARG cc_start: 0.8959 (tpt90) cc_final: 0.8339 (tpp80) REVERT: I 81 ASP cc_start: 0.7191 (p0) cc_final: 0.6910 (p0) REVERT: I 115 MET cc_start: 0.8218 (tpp) cc_final: 0.7715 (mmm) REVERT: N 4 MET cc_start: 0.6015 (mmm) cc_final: 0.4585 (tpp) REVERT: N 162 ARG cc_start: 0.9017 (tpt90) cc_final: 0.8409 (tpp80) REVERT: J 81 ASP cc_start: 0.7330 (p0) cc_final: 0.7051 (p0) REVERT: J 115 MET cc_start: 0.8178 (mmm) cc_final: 0.7844 (mmt) outliers start: 74 outliers final: 50 residues processed: 412 average time/residue: 0.2510 time to fit residues: 160.9330 Evaluate side-chains 311 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 256 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 911 VAL Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1063 LEU Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1013 ILE Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1063 LEU Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 208 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 82 optimal weight: 5.9990 chunk 409 optimal weight: 9.9990 chunk 316 optimal weight: 2.9990 chunk 424 optimal weight: 9.9990 chunk 177 optimal weight: 0.5980 chunk 318 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 179 optimal weight: 0.0570 chunk 365 optimal weight: 20.0000 overall best weight: 2.9304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 440 ASN A 926 GLN A 955 ASN A1011 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 218 GLN B 440 ASN B 762 GLN B 926 GLN ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 ASN C 926 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN M 3 GLN N 3 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.061034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.049405 restraints weight = 358907.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.050631 restraints weight = 179237.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.051337 restraints weight = 110400.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.051821 restraints weight = 79208.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.052121 restraints weight = 63331.518| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 36051 Z= 0.222 Angle : 0.760 12.620 49215 Z= 0.391 Chirality : 0.047 0.270 5766 Planarity : 0.005 0.051 6204 Dihedral : 6.678 55.372 6360 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.93 % Allowed : 7.23 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.22 (0.12), residues: 4353 helix: 1.08 (0.19), residues: 681 sheet: 0.18 (0.13), residues: 1305 loop : -0.05 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 34 TYR 0.041 0.002 TYR A1067 PHE 0.030 0.002 PHE C 782 TRP 0.025 0.002 TRP A 152 HIS 0.010 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00475 (35916) covalent geometry : angle 0.73957 (48867) SS BOND : bond 0.00424 ( 57) SS BOND : angle 1.00706 ( 114) hydrogen bonds : bond 0.05281 ( 1430) hydrogen bonds : angle 6.86302 ( 3897) link_BETA1-4 : bond 0.00539 ( 33) link_BETA1-4 : angle 2.02304 ( 99) link_NAG-ASN : bond 0.00605 ( 45) link_NAG-ASN : angle 2.95201 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 277 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 LYS cc_start: 0.8225 (mmtm) cc_final: 0.7993 (mmtm) REVERT: A 226 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8847 (mt) REVERT: A 513 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8611 (pp) REVERT: A 759 PHE cc_start: 0.8871 (t80) cc_final: 0.8399 (t80) REVERT: A 775 ASP cc_start: 0.8715 (p0) cc_final: 0.8507 (p0) REVERT: A 916 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8586 (pp) REVERT: A 922 LEU cc_start: 0.9545 (mm) cc_final: 0.9285 (mp) REVERT: A 936 ASP cc_start: 0.9093 (m-30) cc_final: 0.8721 (t0) REVERT: A 945 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8995 (pp) REVERT: A 1002 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8201 (tm-30) REVERT: A 1021 SER cc_start: 0.9770 (m) cc_final: 0.9395 (t) REVERT: A 1040 VAL cc_start: 0.9323 (t) cc_final: 0.9077 (p) REVERT: A 1047 TYR cc_start: 0.4077 (OUTLIER) cc_final: 0.3285 (m-80) REVERT: A 1067 TYR cc_start: 0.5932 (m-80) cc_final: 0.5632 (m-80) REVERT: A 1123 SER cc_start: 0.7838 (t) cc_final: 0.7494 (t) REVERT: A 1125 ASN cc_start: 0.8177 (t0) cc_final: 0.7961 (t0) REVERT: B 513 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8566 (pp) REVERT: B 725 GLU cc_start: 0.8373 (tm-30) cc_final: 0.8045 (tm-30) REVERT: B 759 PHE cc_start: 0.8512 (t80) cc_final: 0.8156 (t80) REVERT: B 776 LYS cc_start: 0.9391 (tmtt) cc_final: 0.8884 (tptp) REVERT: B 780 GLU cc_start: 0.9171 (tp30) cc_final: 0.8785 (tp30) REVERT: B 902 MET cc_start: 0.8981 (tpp) cc_final: 0.8625 (tpp) REVERT: B 916 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8274 (pp) REVERT: B 936 ASP cc_start: 0.9121 (m-30) cc_final: 0.8753 (t0) REVERT: B 1001 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9484 (pp) REVERT: B 1123 SER cc_start: 0.7934 (t) cc_final: 0.7566 (t) REVERT: B 1125 ASN cc_start: 0.8115 (t0) cc_final: 0.7880 (t0) REVERT: C 32 PHE cc_start: 0.8434 (t80) cc_final: 0.8049 (t80) REVERT: C 226 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8889 (mt) REVERT: C 513 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8597 (pp) REVERT: C 740 MET cc_start: 0.8698 (mmm) cc_final: 0.8488 (mmm) REVERT: C 775 ASP cc_start: 0.8865 (m-30) cc_final: 0.8572 (m-30) REVERT: C 776 LYS cc_start: 0.9365 (tmtt) cc_final: 0.9137 (tptp) REVERT: C 869 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8738 (ptp) REVERT: C 902 MET cc_start: 0.9199 (mmm) cc_final: 0.8994 (tpp) REVERT: C 936 ASP cc_start: 0.9076 (m-30) cc_final: 0.8721 (t0) REVERT: C 1001 LEU cc_start: 0.9813 (tp) cc_final: 0.9407 (pp) REVERT: C 1002 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8352 (tm-30) REVERT: C 1021 SER cc_start: 0.9694 (m) cc_final: 0.9434 (p) REVERT: C 1038 LYS cc_start: 0.9551 (mttp) cc_final: 0.9227 (mmmt) REVERT: C 1123 SER cc_start: 0.7930 (t) cc_final: 0.7605 (t) REVERT: C 1125 ASN cc_start: 0.8148 (t0) cc_final: 0.7883 (t0) REVERT: L 4 MET cc_start: 0.5915 (mmm) cc_final: 0.5444 (tpp) REVERT: H 39 MET cc_start: 0.5713 (mpp) cc_final: 0.4723 (mmm) REVERT: H 81 ASP cc_start: 0.7468 (p0) cc_final: 0.6922 (p0) REVERT: H 84 LYS cc_start: 0.8866 (tptp) cc_final: 0.8250 (tttt) REVERT: H 159 ASP cc_start: 0.9558 (m-30) cc_final: 0.9231 (p0) REVERT: M 4 MET cc_start: 0.5600 (mmm) cc_final: 0.4918 (tpp) REVERT: I 39 MET cc_start: 0.5530 (mpp) cc_final: 0.4416 (mmm) REVERT: I 91 MET cc_start: 0.7102 (mpp) cc_final: 0.6785 (mpp) REVERT: I 159 ASP cc_start: 0.9574 (m-30) cc_final: 0.9243 (p0) REVERT: N 4 MET cc_start: 0.6065 (mmm) cc_final: 0.5230 (tpp) REVERT: J 91 MET cc_start: 0.7147 (mpp) cc_final: 0.6779 (mpp) REVERT: J 115 MET cc_start: 0.8399 (mmm) cc_final: 0.7937 (mmt) REVERT: J 159 ASP cc_start: 0.9556 (m-30) cc_final: 0.9195 (p0) outliers start: 112 outliers final: 65 residues processed: 367 average time/residue: 0.2361 time to fit residues: 138.2370 Evaluate side-chains 318 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 242 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 801 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 801 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 48 LYS Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 229 LYS Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 48 LYS Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 229 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 48 LYS Chi-restraints excluded: chain J residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 378 optimal weight: 0.1980 chunk 136 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 398 optimal weight: 5.9990 chunk 373 optimal weight: 30.0000 chunk 349 optimal weight: 0.5980 chunk 357 optimal weight: 2.9990 chunk 421 optimal weight: 20.0000 chunk 307 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 762 GLN B 926 GLN B 955 ASN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN C 762 GLN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1113 GLN C1119 ASN L 3 GLN L 108 HIS ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 108 HIS ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 108 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.060211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.048511 restraints weight = 357627.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.049729 restraints weight = 178033.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.050429 restraints weight = 109517.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.050923 restraints weight = 78618.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.051173 restraints weight = 62137.970| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 36051 Z= 0.188 Angle : 0.694 12.034 49215 Z= 0.355 Chirality : 0.046 0.284 5766 Planarity : 0.004 0.049 6204 Dihedral : 6.056 55.913 6358 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.83 % Favored : 97.11 % Rotamer: Outliers : 2.96 % Allowed : 8.48 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.19 (0.13), residues: 4353 helix: 1.11 (0.19), residues: 687 sheet: 0.13 (0.14), residues: 1281 loop : -0.07 (0.13), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 20 TYR 0.028 0.002 TYR A1067 PHE 0.025 0.002 PHE A 32 TRP 0.016 0.002 TRP A 152 HIS 0.008 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00404 (35916) covalent geometry : angle 0.67353 (48867) SS BOND : bond 0.00382 ( 57) SS BOND : angle 0.99608 ( 114) hydrogen bonds : bond 0.04790 ( 1430) hydrogen bonds : angle 6.58198 ( 3897) link_BETA1-4 : bond 0.00559 ( 33) link_BETA1-4 : angle 1.92496 ( 99) link_NAG-ASN : bond 0.00454 ( 45) link_NAG-ASN : angle 2.80246 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 240 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 226 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9020 (mt) REVERT: A 513 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8629 (pp) REVERT: A 725 GLU cc_start: 0.8579 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 759 PHE cc_start: 0.8637 (t80) cc_final: 0.8362 (t80) REVERT: A 869 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8820 (ptp) REVERT: A 902 MET cc_start: 0.9457 (mmm) cc_final: 0.9252 (tpp) REVERT: A 936 ASP cc_start: 0.9118 (m-30) cc_final: 0.8745 (t0) REVERT: A 1001 LEU cc_start: 0.9772 (tt) cc_final: 0.9503 (pp) REVERT: A 1002 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8384 (tm-30) REVERT: A 1021 SER cc_start: 0.9763 (m) cc_final: 0.9520 (p) REVERT: A 1029 MET cc_start: 0.7723 (tmm) cc_final: 0.7496 (tmm) REVERT: A 1040 VAL cc_start: 0.9445 (t) cc_final: 0.8914 (m) REVERT: A 1047 TYR cc_start: 0.4507 (OUTLIER) cc_final: 0.4188 (m-80) REVERT: A 1050 MET cc_start: 0.8751 (mtp) cc_final: 0.8499 (mtp) REVERT: A 1123 SER cc_start: 0.7889 (t) cc_final: 0.7548 (t) REVERT: A 1125 ASN cc_start: 0.8235 (t0) cc_final: 0.8001 (t0) REVERT: B 513 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8631 (pp) REVERT: B 725 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8264 (tm-30) REVERT: B 759 PHE cc_start: 0.8660 (t80) cc_final: 0.8203 (t80) REVERT: B 776 LYS cc_start: 0.9443 (tmtt) cc_final: 0.9024 (tptp) REVERT: B 780 GLU cc_start: 0.9150 (tp30) cc_final: 0.8813 (tp30) REVERT: B 781 VAL cc_start: 0.9372 (t) cc_final: 0.9139 (m) REVERT: B 916 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8508 (pp) REVERT: B 936 ASP cc_start: 0.9123 (m-30) cc_final: 0.8773 (t0) REVERT: B 1001 LEU cc_start: 0.9791 (OUTLIER) cc_final: 0.9491 (pp) REVERT: B 1123 SER cc_start: 0.8070 (t) cc_final: 0.7695 (t) REVERT: B 1125 ASN cc_start: 0.8216 (t0) cc_final: 0.7926 (t0) REVERT: C 175 PHE cc_start: 0.9568 (m-80) cc_final: 0.9235 (m-80) REVERT: C 226 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9077 (mt) REVERT: C 513 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8699 (pp) REVERT: C 759 PHE cc_start: 0.8390 (OUTLIER) cc_final: 0.7775 (t80) REVERT: C 775 ASP cc_start: 0.8848 (m-30) cc_final: 0.8528 (m-30) REVERT: C 869 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8799 (ptp) REVERT: C 902 MET cc_start: 0.9247 (mmm) cc_final: 0.8690 (tpp) REVERT: C 936 ASP cc_start: 0.9086 (m-30) cc_final: 0.8748 (t0) REVERT: C 1001 LEU cc_start: 0.9842 (tp) cc_final: 0.9355 (pp) REVERT: C 1002 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8390 (tm-30) REVERT: C 1017 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8785 (pp20) REVERT: C 1031 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8412 (mm-30) REVERT: C 1038 LYS cc_start: 0.9581 (mttp) cc_final: 0.9173 (mmmt) REVERT: C 1050 MET cc_start: 0.8718 (mtp) cc_final: 0.8346 (mtp) REVERT: C 1123 SER cc_start: 0.8001 (t) cc_final: 0.7664 (t) REVERT: C 1125 ASN cc_start: 0.8260 (t0) cc_final: 0.7981 (t0) REVERT: L 4 MET cc_start: 0.6109 (mmm) cc_final: 0.5352 (tpp) REVERT: L 11 LEU cc_start: 0.9294 (tp) cc_final: 0.8975 (pp) REVERT: L 162 ARG cc_start: 0.9112 (tpt90) cc_final: 0.8558 (tpp80) REVERT: H 39 MET cc_start: 0.5725 (mpp) cc_final: 0.4776 (mmm) REVERT: H 81 ASP cc_start: 0.7541 (p0) cc_final: 0.6882 (p0) REVERT: H 84 LYS cc_start: 0.8879 (tptp) cc_final: 0.8274 (tttt) REVERT: H 115 MET cc_start: 0.7837 (mmm) cc_final: 0.7520 (tpp) REVERT: H 159 ASP cc_start: 0.9535 (m-30) cc_final: 0.9163 (p0) REVERT: M 4 MET cc_start: 0.5771 (mmm) cc_final: 0.5427 (tpp) REVERT: M 11 LEU cc_start: 0.9247 (tp) cc_final: 0.8971 (pp) REVERT: M 162 ARG cc_start: 0.9117 (tpt90) cc_final: 0.8620 (tpp80) REVERT: I 39 MET cc_start: 0.5571 (mpp) cc_final: 0.4504 (mmm) REVERT: I 91 MET cc_start: 0.7087 (mpp) cc_final: 0.6715 (mpp) REVERT: I 115 MET cc_start: 0.7071 (tpp) cc_final: 0.6301 (tpp) REVERT: I 159 ASP cc_start: 0.9584 (m-30) cc_final: 0.9256 (p0) REVERT: N 4 MET cc_start: 0.6393 (mmm) cc_final: 0.5835 (tpp) REVERT: N 11 LEU cc_start: 0.9285 (tp) cc_final: 0.8914 (pp) REVERT: N 162 ARG cc_start: 0.9128 (tpt90) cc_final: 0.8624 (tpp80) REVERT: J 91 MET cc_start: 0.6997 (mpp) cc_final: 0.6489 (mpp) REVERT: J 115 MET cc_start: 0.8430 (mmm) cc_final: 0.7935 (mmt) REVERT: J 159 ASP cc_start: 0.9516 (m-30) cc_final: 0.9158 (p0) outliers start: 113 outliers final: 61 residues processed: 338 average time/residue: 0.2378 time to fit residues: 127.2085 Evaluate side-chains 288 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 216 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1047 TYR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 709 ASN Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 664 ILE Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1113 GLN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 221 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 221 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 314 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 270 optimal weight: 10.0000 chunk 257 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 chunk 376 optimal weight: 9.9990 chunk 413 optimal weight: 9.9990 chunk 191 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 chunk 211 optimal weight: 2.9990 chunk 380 optimal weight: 30.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 115 GLN A 239 GLN A 913 GLN A 926 GLN A 935 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN A1119 ASN B 66 HIS B 115 GLN B 913 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS C 115 GLN C 907 ASN C 913 GLN C 926 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN L 209 HIS L 219 GLN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 167 GLN M 209 HIS ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 167 GLN N 209 HIS J 186 GLN ** J 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.051104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.036133 restraints weight = 307845.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.037249 restraints weight = 176248.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.037987 restraints weight = 119205.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.038495 restraints weight = 90317.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.038843 restraints weight = 73924.146| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.141 36051 Z= 0.331 Angle : 0.811 10.896 49215 Z= 0.418 Chirality : 0.047 0.297 5766 Planarity : 0.005 0.068 6204 Dihedral : 6.399 57.031 6356 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 23.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.18 % Favored : 95.75 % Rotamer: Outliers : 2.85 % Allowed : 9.71 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.16 (0.13), residues: 4353 helix: 0.69 (0.19), residues: 711 sheet: -0.05 (0.14), residues: 1272 loop : -0.29 (0.13), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 567 TYR 0.039 0.002 TYR A1067 PHE 0.041 0.003 PHE C 32 TRP 0.017 0.002 TRP C1102 HIS 0.014 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00687 (35916) covalent geometry : angle 0.78829 (48867) SS BOND : bond 0.00559 ( 57) SS BOND : angle 1.21606 ( 114) hydrogen bonds : bond 0.05464 ( 1430) hydrogen bonds : angle 6.92387 ( 3897) link_BETA1-4 : bond 0.00578 ( 33) link_BETA1-4 : angle 2.17065 ( 99) link_NAG-ASN : bond 0.00611 ( 45) link_NAG-ASN : angle 3.19447 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 218 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9198 (mt) REVERT: A 513 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8862 (pp) REVERT: A 725 GLU cc_start: 0.8625 (tm-30) cc_final: 0.8046 (tm-30) REVERT: A 740 MET cc_start: 0.8931 (mmm) cc_final: 0.8396 (mmt) REVERT: A 759 PHE cc_start: 0.8706 (t80) cc_final: 0.8297 (t80) REVERT: A 869 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.9148 (ptp) REVERT: A 936 ASP cc_start: 0.9300 (m-30) cc_final: 0.8975 (t0) REVERT: A 1001 LEU cc_start: 0.9760 (tt) cc_final: 0.9538 (pp) REVERT: A 1038 LYS cc_start: 0.9538 (mttt) cc_final: 0.9288 (mmmt) REVERT: A 1067 TYR cc_start: 0.6474 (m-80) cc_final: 0.5974 (m-80) REVERT: A 1123 SER cc_start: 0.8350 (t) cc_final: 0.8028 (t) REVERT: A 1125 ASN cc_start: 0.8348 (t0) cc_final: 0.8114 (t0) REVERT: A 1138 TYR cc_start: 0.7996 (m-80) cc_final: 0.7794 (m-80) REVERT: B 513 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8941 (pp) REVERT: B 776 LYS cc_start: 0.9405 (tmtt) cc_final: 0.8850 (tptp) REVERT: B 780 GLU cc_start: 0.9140 (tp30) cc_final: 0.8604 (tp30) REVERT: B 916 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8715 (pp) REVERT: B 936 ASP cc_start: 0.9251 (m-30) cc_final: 0.8926 (t0) REVERT: B 1001 LEU cc_start: 0.9808 (OUTLIER) cc_final: 0.9533 (pp) REVERT: B 1040 VAL cc_start: 0.9464 (t) cc_final: 0.9248 (p) REVERT: B 1050 MET cc_start: 0.8774 (mtp) cc_final: 0.8339 (mtp) REVERT: B 1092 GLU cc_start: 0.8218 (mp0) cc_final: 0.7878 (pm20) REVERT: B 1123 SER cc_start: 0.8476 (t) cc_final: 0.8185 (t) REVERT: B 1125 ASN cc_start: 0.8408 (t0) cc_final: 0.8130 (t0) REVERT: B 1138 TYR cc_start: 0.7902 (m-80) cc_final: 0.7684 (m-80) REVERT: C 104 TRP cc_start: 0.8796 (m-90) cc_final: 0.8541 (m-90) REVERT: C 226 LEU cc_start: 0.9570 (OUTLIER) cc_final: 0.9198 (mt) REVERT: C 513 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8882 (pp) REVERT: C 725 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8095 (tm-30) REVERT: C 740 MET cc_start: 0.8892 (mmm) cc_final: 0.8407 (mmt) REVERT: C 780 GLU cc_start: 0.9044 (tp30) cc_final: 0.8821 (tt0) REVERT: C 869 MET cc_start: 0.9319 (OUTLIER) cc_final: 0.8979 (ptp) REVERT: C 902 MET cc_start: 0.9320 (mmm) cc_final: 0.9027 (tpp) REVERT: C 936 ASP cc_start: 0.9247 (m-30) cc_final: 0.8896 (t0) REVERT: C 1002 GLN cc_start: 0.8916 (tm-30) cc_final: 0.8461 (tm-30) REVERT: C 1005 GLN cc_start: 0.9410 (mm-40) cc_final: 0.9179 (mm-40) REVERT: C 1031 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8550 (mm-30) REVERT: C 1038 LYS cc_start: 0.9548 (mttp) cc_final: 0.9150 (mmmt) REVERT: C 1113 GLN cc_start: 0.9412 (tt0) cc_final: 0.9192 (tm-30) REVERT: C 1123 SER cc_start: 0.8322 (t) cc_final: 0.8011 (t) REVERT: C 1125 ASN cc_start: 0.8481 (t0) cc_final: 0.8234 (t0) REVERT: L 4 MET cc_start: 0.7032 (mmm) cc_final: 0.6108 (tpp) REVERT: L 11 LEU cc_start: 0.9278 (tp) cc_final: 0.8938 (pt) REVERT: H 39 MET cc_start: 0.5372 (mpp) cc_final: 0.4742 (mmm) REVERT: H 81 ASP cc_start: 0.7627 (p0) cc_final: 0.7019 (p0) REVERT: H 84 LYS cc_start: 0.8928 (tptp) cc_final: 0.8295 (tttp) REVERT: H 115 MET cc_start: 0.8020 (mmm) cc_final: 0.7586 (tpp) REVERT: H 159 ASP cc_start: 0.9500 (m-30) cc_final: 0.9053 (p0) REVERT: M 4 MET cc_start: 0.7187 (mmm) cc_final: 0.5993 (tpp) REVERT: M 11 LEU cc_start: 0.9268 (tp) cc_final: 0.8858 (pt) REVERT: I 39 MET cc_start: 0.5399 (mpp) cc_final: 0.4604 (mmm) REVERT: I 115 MET cc_start: 0.7428 (tpp) cc_final: 0.6790 (tpp) REVERT: I 159 ASP cc_start: 0.9496 (m-30) cc_final: 0.9109 (p0) REVERT: N 4 MET cc_start: 0.6795 (mmm) cc_final: 0.5700 (tpp) REVERT: N 11 LEU cc_start: 0.9263 (tp) cc_final: 0.8852 (pt) REVERT: J 91 MET cc_start: 0.7033 (mpp) cc_final: 0.6582 (mpp) REVERT: J 115 MET cc_start: 0.8576 (mmm) cc_final: 0.8146 (mmt) REVERT: J 159 ASP cc_start: 0.9516 (m-30) cc_final: 0.9125 (p0) outliers start: 109 outliers final: 71 residues processed: 304 average time/residue: 0.2467 time to fit residues: 118.9341 Evaluate side-chains 271 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 191 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 1013 ILE Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 265 TYR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 208 THR Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 208 THR Chi-restraints excluded: chain I residue 221 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 84 LYS Chi-restraints excluded: chain J residue 208 THR Chi-restraints excluded: chain J residue 221 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 414 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 280 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 75 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 299 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 935 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN I 186 GLN ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** J 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.053051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.037637 restraints weight = 295707.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.038870 restraints weight = 165672.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.039689 restraints weight = 110825.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.040254 restraints weight = 83172.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.040630 restraints weight = 67399.725| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.5837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 36051 Z= 0.138 Angle : 0.668 11.908 49215 Z= 0.338 Chirality : 0.046 0.289 5766 Planarity : 0.004 0.049 6204 Dihedral : 5.905 55.639 6354 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.65 % Rotamer: Outliers : 2.04 % Allowed : 11.36 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.01 (0.13), residues: 4353 helix: 1.09 (0.20), residues: 684 sheet: 0.01 (0.14), residues: 1206 loop : -0.23 (0.13), residues: 2463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1107 TYR 0.028 0.002 TYR A 904 PHE 0.024 0.002 PHE C 32 TRP 0.014 0.002 TRP B 436 HIS 0.010 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00310 (35916) covalent geometry : angle 0.65042 (48867) SS BOND : bond 0.00363 ( 57) SS BOND : angle 0.92415 ( 114) hydrogen bonds : bond 0.04416 ( 1430) hydrogen bonds : angle 6.42095 ( 3897) link_BETA1-4 : bond 0.00542 ( 33) link_BETA1-4 : angle 1.77995 ( 99) link_NAG-ASN : bond 0.00476 ( 45) link_NAG-ASN : angle 2.54683 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 234 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9188 (mt) REVERT: A 513 LEU cc_start: 0.9127 (tp) cc_final: 0.8748 (pp) REVERT: A 740 MET cc_start: 0.8681 (mmm) cc_final: 0.8329 (mmt) REVERT: A 759 PHE cc_start: 0.8638 (t80) cc_final: 0.8191 (t80) REVERT: A 780 GLU cc_start: 0.9115 (tp30) cc_final: 0.8740 (tt0) REVERT: A 869 MET cc_start: 0.9307 (mtp) cc_final: 0.8854 (ptp) REVERT: A 904 TYR cc_start: 0.8940 (m-10) cc_final: 0.8711 (m-10) REVERT: A 916 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8492 (pp) REVERT: A 936 ASP cc_start: 0.9237 (m-30) cc_final: 0.8853 (t0) REVERT: A 1001 LEU cc_start: 0.9793 (tt) cc_final: 0.9538 (pp) REVERT: A 1021 SER cc_start: 0.9755 (m) cc_final: 0.9527 (p) REVERT: A 1123 SER cc_start: 0.8314 (t) cc_final: 0.7987 (t) REVERT: A 1125 ASN cc_start: 0.8350 (t0) cc_final: 0.8105 (t0) REVERT: B 104 TRP cc_start: 0.8675 (m-90) cc_final: 0.8469 (m-90) REVERT: B 513 LEU cc_start: 0.9188 (tp) cc_final: 0.8852 (pp) REVERT: B 776 LYS cc_start: 0.9448 (tmtt) cc_final: 0.8925 (tptp) REVERT: B 780 GLU cc_start: 0.9181 (tp30) cc_final: 0.8722 (tp30) REVERT: B 781 VAL cc_start: 0.9436 (t) cc_final: 0.9148 (m) REVERT: B 869 MET cc_start: 0.9270 (mtp) cc_final: 0.9027 (ptp) REVERT: B 916 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8387 (pp) REVERT: B 936 ASP cc_start: 0.9204 (m-30) cc_final: 0.8869 (t0) REVERT: B 1001 LEU cc_start: 0.9813 (OUTLIER) cc_final: 0.9502 (pp) REVERT: B 1123 SER cc_start: 0.8200 (t) cc_final: 0.7882 (t) REVERT: B 1125 ASN cc_start: 0.8307 (t0) cc_final: 0.8013 (t0) REVERT: C 104 TRP cc_start: 0.8605 (m-90) cc_final: 0.8392 (m-90) REVERT: C 226 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9273 (mt) REVERT: C 513 LEU cc_start: 0.9160 (tp) cc_final: 0.8784 (pp) REVERT: C 740 MET cc_start: 0.8548 (mmm) cc_final: 0.8236 (mmt) REVERT: C 773 GLU cc_start: 0.9148 (tt0) cc_final: 0.8379 (tm-30) REVERT: C 796 ASP cc_start: 0.8842 (m-30) cc_final: 0.8537 (p0) REVERT: C 869 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8800 (ptp) REVERT: C 902 MET cc_start: 0.9346 (mmm) cc_final: 0.9040 (tpp) REVERT: C 936 ASP cc_start: 0.9204 (m-30) cc_final: 0.8844 (t0) REVERT: C 954 GLN cc_start: 0.9343 (mt0) cc_final: 0.9064 (pt0) REVERT: C 1002 GLN cc_start: 0.8982 (tm-30) cc_final: 0.8336 (tm-30) REVERT: C 1017 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8777 (pp20) REVERT: C 1038 LYS cc_start: 0.9541 (mttp) cc_final: 0.9307 (mttp) REVERT: C 1123 SER cc_start: 0.8236 (t) cc_final: 0.7936 (t) REVERT: C 1125 ASN cc_start: 0.8372 (t0) cc_final: 0.8095 (t0) REVERT: C 1138 TYR cc_start: 0.7578 (m-80) cc_final: 0.7371 (m-80) REVERT: L 4 MET cc_start: 0.7319 (mmm) cc_final: 0.6784 (tpp) REVERT: L 11 LEU cc_start: 0.9221 (tp) cc_final: 0.8893 (pt) REVERT: L 162 ARG cc_start: 0.9080 (tpt90) cc_final: 0.8575 (tpp80) REVERT: H 39 MET cc_start: 0.5410 (mpp) cc_final: 0.4669 (mmm) REVERT: H 81 ASP cc_start: 0.7580 (p0) cc_final: 0.7042 (p0) REVERT: H 84 LYS cc_start: 0.8899 (tptp) cc_final: 0.8296 (tttt) REVERT: H 115 MET cc_start: 0.7691 (mmm) cc_final: 0.7210 (tpp) REVERT: H 159 ASP cc_start: 0.9493 (m-30) cc_final: 0.9041 (p0) REVERT: M 4 MET cc_start: 0.6998 (mmm) cc_final: 0.6028 (tpp) REVERT: M 11 LEU cc_start: 0.9261 (tp) cc_final: 0.8887 (pt) REVERT: I 39 MET cc_start: 0.5451 (mpp) cc_final: 0.4434 (mmm) REVERT: I 115 MET cc_start: 0.7287 (tpp) cc_final: 0.6633 (tpp) REVERT: I 159 ASP cc_start: 0.9525 (m-30) cc_final: 0.9172 (p0) REVERT: I 225 LYS cc_start: 0.9496 (tmmt) cc_final: 0.9241 (tppt) REVERT: N 4 MET cc_start: 0.6874 (mmm) cc_final: 0.6127 (tpp) REVERT: N 11 LEU cc_start: 0.9182 (tp) cc_final: 0.8830 (pt) REVERT: J 91 MET cc_start: 0.7037 (mpp) cc_final: 0.6603 (mpp) REVERT: J 115 MET cc_start: 0.8460 (mmm) cc_final: 0.8064 (mmt) REVERT: J 159 ASP cc_start: 0.9510 (m-30) cc_final: 0.9111 (p0) outliers start: 78 outliers final: 52 residues processed: 301 average time/residue: 0.2415 time to fit residues: 117.4512 Evaluate side-chains 266 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 916 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 221 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 403 optimal weight: 5.9990 chunk 250 optimal weight: 10.0000 chunk 247 optimal weight: 0.0060 chunk 289 optimal weight: 0.5980 chunk 414 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 308 optimal weight: 0.8980 overall best weight: 2.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 926 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1113 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 219 GLN ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 219 GLN ** J 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.051889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.036592 restraints weight = 303447.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.037784 restraints weight = 170621.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.038570 restraints weight = 114451.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.039110 restraints weight = 86209.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.039463 restraints weight = 70145.480| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.6195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 36051 Z= 0.189 Angle : 0.671 10.795 49215 Z= 0.339 Chirality : 0.045 0.267 5766 Planarity : 0.004 0.047 6204 Dihedral : 5.720 56.749 6354 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.80 % Rotamer: Outliers : 1.96 % Allowed : 12.54 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: 0.00 (0.13), residues: 4353 helix: 1.26 (0.20), residues: 684 sheet: -0.00 (0.14), residues: 1224 loop : -0.29 (0.13), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C1019 TYR 0.023 0.002 TYR B1067 PHE 0.025 0.002 PHE B1052 TRP 0.035 0.002 TRP A 104 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00411 (35916) covalent geometry : angle 0.65222 (48867) SS BOND : bond 0.00405 ( 57) SS BOND : angle 0.96255 ( 114) hydrogen bonds : bond 0.04456 ( 1430) hydrogen bonds : angle 6.37917 ( 3897) link_BETA1-4 : bond 0.00512 ( 33) link_BETA1-4 : angle 1.84027 ( 99) link_NAG-ASN : bond 0.00495 ( 45) link_NAG-ASN : angle 2.62475 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 216 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.8593 (m-90) cc_final: 0.8322 (m-90) REVERT: A 226 LEU cc_start: 0.9594 (OUTLIER) cc_final: 0.9220 (mt) REVERT: A 309 GLU cc_start: 0.9019 (pm20) cc_final: 0.8654 (pm20) REVERT: A 513 LEU cc_start: 0.9148 (tp) cc_final: 0.8761 (pp) REVERT: A 740 MET cc_start: 0.8745 (mmm) cc_final: 0.8280 (mmt) REVERT: A 759 PHE cc_start: 0.8653 (t80) cc_final: 0.8215 (t80) REVERT: A 780 GLU cc_start: 0.9059 (tp30) cc_final: 0.8688 (tt0) REVERT: A 869 MET cc_start: 0.9342 (mtp) cc_final: 0.8884 (ptp) REVERT: A 936 ASP cc_start: 0.9221 (m-30) cc_final: 0.8909 (t0) REVERT: A 1001 LEU cc_start: 0.9795 (tt) cc_final: 0.9560 (pp) REVERT: A 1002 GLN cc_start: 0.8916 (tp40) cc_final: 0.8612 (tm-30) REVERT: A 1123 SER cc_start: 0.8296 (t) cc_final: 0.7959 (t) REVERT: A 1125 ASN cc_start: 0.8422 (t0) cc_final: 0.8154 (t0) REVERT: B 104 TRP cc_start: 0.8725 (m-90) cc_final: 0.8508 (m-90) REVERT: B 513 LEU cc_start: 0.9207 (tp) cc_final: 0.8872 (pp) REVERT: B 776 LYS cc_start: 0.9433 (tmtt) cc_final: 0.8842 (tptp) REVERT: B 780 GLU cc_start: 0.9127 (tp30) cc_final: 0.8676 (tp30) REVERT: B 781 VAL cc_start: 0.9438 (t) cc_final: 0.9135 (m) REVERT: B 796 ASP cc_start: 0.8839 (m-30) cc_final: 0.8554 (p0) REVERT: B 869 MET cc_start: 0.9309 (mtp) cc_final: 0.9076 (ptp) REVERT: B 936 ASP cc_start: 0.9204 (m-30) cc_final: 0.8902 (t0) REVERT: B 1001 LEU cc_start: 0.9815 (tt) cc_final: 0.9514 (pp) REVERT: B 1031 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7670 (tt0) REVERT: B 1038 LYS cc_start: 0.9494 (mttt) cc_final: 0.8823 (ptmt) REVERT: B 1123 SER cc_start: 0.8256 (t) cc_final: 0.7939 (t) REVERT: B 1125 ASN cc_start: 0.8407 (t0) cc_final: 0.8088 (t0) REVERT: C 104 TRP cc_start: 0.8651 (m-90) cc_final: 0.8406 (m-90) REVERT: C 226 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9264 (mt) REVERT: C 513 LEU cc_start: 0.9190 (tp) cc_final: 0.8828 (pp) REVERT: C 740 MET cc_start: 0.8563 (mmm) cc_final: 0.8244 (mmt) REVERT: C 759 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7664 (t80) REVERT: C 796 ASP cc_start: 0.8790 (m-30) cc_final: 0.8556 (p0) REVERT: C 869 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.8934 (ptp) REVERT: C 936 ASP cc_start: 0.9179 (m-30) cc_final: 0.8854 (t0) REVERT: C 954 GLN cc_start: 0.9324 (mt0) cc_final: 0.9085 (pt0) REVERT: C 1001 LEU cc_start: 0.9858 (tp) cc_final: 0.9451 (pp) REVERT: C 1002 GLN cc_start: 0.8973 (tm-30) cc_final: 0.8480 (tm-30) REVERT: C 1005 GLN cc_start: 0.9457 (mm-40) cc_final: 0.9043 (mm-40) REVERT: C 1012 LEU cc_start: 0.9861 (OUTLIER) cc_final: 0.9568 (mm) REVERT: C 1017 GLU cc_start: 0.8980 (tm-30) cc_final: 0.8768 (pp20) REVERT: C 1031 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8537 (mm-30) REVERT: C 1038 LYS cc_start: 0.9452 (mttp) cc_final: 0.9232 (ttmt) REVERT: C 1123 SER cc_start: 0.8215 (t) cc_final: 0.7901 (t) REVERT: C 1125 ASN cc_start: 0.8405 (t0) cc_final: 0.8109 (t0) REVERT: L 4 MET cc_start: 0.7494 (mmm) cc_final: 0.6636 (tpp) REVERT: L 11 LEU cc_start: 0.9232 (tp) cc_final: 0.8883 (pt) REVERT: L 162 ARG cc_start: 0.9150 (tpt90) cc_final: 0.8649 (tpp80) REVERT: H 39 MET cc_start: 0.5408 (mpp) cc_final: 0.4618 (mmm) REVERT: H 115 MET cc_start: 0.7590 (mmm) cc_final: 0.7057 (tpp) REVERT: H 159 ASP cc_start: 0.9510 (m-30) cc_final: 0.9079 (p0) REVERT: M 4 MET cc_start: 0.7315 (mmm) cc_final: 0.6128 (tpp) REVERT: M 11 LEU cc_start: 0.9178 (tp) cc_final: 0.8789 (pt) REVERT: M 162 ARG cc_start: 0.9141 (tpt90) cc_final: 0.8649 (tpp80) REVERT: I 39 MET cc_start: 0.5503 (mpp) cc_final: 0.4535 (mmm) REVERT: I 115 MET cc_start: 0.7214 (tpp) cc_final: 0.6536 (tpp) REVERT: I 159 ASP cc_start: 0.9531 (m-30) cc_final: 0.9173 (p0) REVERT: I 225 LYS cc_start: 0.9506 (tmmt) cc_final: 0.9229 (tppt) REVERT: N 4 MET cc_start: 0.7070 (mmm) cc_final: 0.6148 (tpp) REVERT: N 11 LEU cc_start: 0.9247 (tp) cc_final: 0.8887 (pt) REVERT: N 162 ARG cc_start: 0.9165 (tpt90) cc_final: 0.8690 (tpp80) REVERT: J 91 MET cc_start: 0.6965 (mpp) cc_final: 0.6548 (mpp) REVERT: J 115 MET cc_start: 0.8492 (mmm) cc_final: 0.8146 (mmt) REVERT: J 159 ASP cc_start: 0.9498 (m-30) cc_final: 0.9063 (p0) outliers start: 75 outliers final: 55 residues processed: 280 average time/residue: 0.2438 time to fit residues: 109.6734 Evaluate side-chains 257 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 197 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1113 GLN Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1074 ASN Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain L residue 3 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 221 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 29 optimal weight: 30.0000 chunk 222 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 302 optimal weight: 9.9990 chunk 350 optimal weight: 7.9990 chunk 260 optimal weight: 0.8980 chunk 403 optimal weight: 5.9990 chunk 290 optimal weight: 0.9980 chunk 253 optimal weight: 4.9990 chunk 351 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 872 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1113 GLN B 30 ASN B 935 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 30 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 186 GLN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.050745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.035643 restraints weight = 313058.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.036824 restraints weight = 172914.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.037594 restraints weight = 114821.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.038114 restraints weight = 86104.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.038457 restraints weight = 70070.780| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.6612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 36051 Z= 0.256 Angle : 0.708 10.415 49215 Z= 0.361 Chirality : 0.045 0.275 5766 Planarity : 0.005 0.045 6204 Dihedral : 5.917 56.536 6354 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.50 % Favored : 95.43 % Rotamer: Outliers : 2.02 % Allowed : 12.94 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: -0.13 (0.13), residues: 4353 helix: 1.08 (0.20), residues: 684 sheet: -0.09 (0.14), residues: 1254 loop : -0.35 (0.13), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1039 TYR 0.028 0.002 TYR A1110 PHE 0.022 0.002 PHE A 906 TRP 0.025 0.002 TRP A 104 HIS 0.010 0.002 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00546 (35916) covalent geometry : angle 0.68908 (48867) SS BOND : bond 0.00475 ( 57) SS BOND : angle 1.02566 ( 114) hydrogen bonds : bond 0.04675 ( 1430) hydrogen bonds : angle 6.51434 ( 3897) link_BETA1-4 : bond 0.00516 ( 33) link_BETA1-4 : angle 1.87465 ( 99) link_NAG-ASN : bond 0.00518 ( 45) link_NAG-ASN : angle 2.73721 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 186 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9239 (mt) REVERT: A 309 GLU cc_start: 0.9116 (pm20) cc_final: 0.8748 (pm20) REVERT: A 740 MET cc_start: 0.8769 (mmm) cc_final: 0.8387 (mmt) REVERT: A 759 PHE cc_start: 0.8734 (t80) cc_final: 0.8248 (t80) REVERT: A 780 GLU cc_start: 0.9002 (tp30) cc_final: 0.8671 (tt0) REVERT: A 936 ASP cc_start: 0.9245 (m-30) cc_final: 0.8929 (t0) REVERT: A 1001 LEU cc_start: 0.9805 (tt) cc_final: 0.9571 (pp) REVERT: A 1123 SER cc_start: 0.8410 (t) cc_final: 0.8097 (t) REVERT: A 1125 ASN cc_start: 0.8606 (t0) cc_final: 0.8302 (t0) REVERT: B 104 TRP cc_start: 0.8760 (m-90) cc_final: 0.8506 (m-90) REVERT: B 776 LYS cc_start: 0.9418 (tmtt) cc_final: 0.8825 (tptp) REVERT: B 780 GLU cc_start: 0.9100 (tp30) cc_final: 0.8672 (tp30) REVERT: B 796 ASP cc_start: 0.8865 (m-30) cc_final: 0.8565 (p0) REVERT: B 869 MET cc_start: 0.9307 (mtp) cc_final: 0.9063 (ptp) REVERT: B 936 ASP cc_start: 0.9231 (m-30) cc_final: 0.8937 (t0) REVERT: B 1001 LEU cc_start: 0.9822 (OUTLIER) cc_final: 0.9522 (pp) REVERT: B 1031 GLU cc_start: 0.8569 (mt-10) cc_final: 0.7721 (tt0) REVERT: B 1123 SER cc_start: 0.8379 (t) cc_final: 0.8071 (t) REVERT: B 1125 ASN cc_start: 0.8473 (t0) cc_final: 0.8135 (t0) REVERT: C 104 TRP cc_start: 0.8684 (m-90) cc_final: 0.8426 (m-90) REVERT: C 226 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9286 (mt) REVERT: C 740 MET cc_start: 0.8614 (mmm) cc_final: 0.8359 (mmt) REVERT: C 773 GLU cc_start: 0.9276 (tt0) cc_final: 0.8300 (tm-30) REVERT: C 796 ASP cc_start: 0.8805 (m-30) cc_final: 0.8561 (p0) REVERT: C 869 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.8975 (ptp) REVERT: C 936 ASP cc_start: 0.9216 (m-30) cc_final: 0.8919 (t0) REVERT: C 954 GLN cc_start: 0.9346 (mt0) cc_final: 0.9116 (pt0) REVERT: C 1001 LEU cc_start: 0.9859 (tp) cc_final: 0.9476 (pp) REVERT: C 1002 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8508 (tm-30) REVERT: C 1017 GLU cc_start: 0.9071 (tm-30) cc_final: 0.8852 (pp20) REVERT: C 1031 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8525 (mm-30) REVERT: C 1123 SER cc_start: 0.8307 (t) cc_final: 0.7998 (t) REVERT: C 1125 ASN cc_start: 0.8449 (t0) cc_final: 0.8154 (t0) REVERT: L 1 ASP cc_start: 0.8483 (m-30) cc_final: 0.8207 (t0) REVERT: L 4 MET cc_start: 0.7896 (mmm) cc_final: 0.6749 (tpp) REVERT: L 11 LEU cc_start: 0.9210 (tp) cc_final: 0.8795 (pt) REVERT: H 39 MET cc_start: 0.5320 (mpp) cc_final: 0.4626 (mmm) REVERT: H 115 MET cc_start: 0.7619 (mmm) cc_final: 0.7109 (tpp) REVERT: H 159 ASP cc_start: 0.9535 (m-30) cc_final: 0.9134 (p0) REVERT: M 4 MET cc_start: 0.7618 (mmm) cc_final: 0.6700 (tpp) REVERT: M 11 LEU cc_start: 0.9142 (tp) cc_final: 0.8785 (pt) REVERT: I 39 MET cc_start: 0.5457 (mpp) cc_final: 0.4583 (mmm) REVERT: I 115 MET cc_start: 0.7310 (tpp) cc_final: 0.6647 (tpp) REVERT: I 159 ASP cc_start: 0.9553 (m-30) cc_final: 0.9216 (p0) REVERT: I 225 LYS cc_start: 0.9506 (tmmt) cc_final: 0.9227 (tppt) REVERT: N 4 MET cc_start: 0.7335 (mmm) cc_final: 0.6444 (tpp) REVERT: N 11 LEU cc_start: 0.9251 (tp) cc_final: 0.8840 (pt) REVERT: J 91 MET cc_start: 0.7023 (mpp) cc_final: 0.6623 (mpp) REVERT: J 115 MET cc_start: 0.8494 (mmm) cc_final: 0.8200 (mmt) REVERT: J 159 ASP cc_start: 0.9532 (m-30) cc_final: 0.9145 (p0) outliers start: 77 outliers final: 63 residues processed: 250 average time/residue: 0.2388 time to fit residues: 95.9885 Evaluate side-chains 246 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 179 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 PHE Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1041 ASP Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain A residue 1121 PHE Chi-restraints excluded: chain B residue 43 PHE Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 43 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 565 PHE Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1041 ASP Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 221 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 431 optimal weight: 5.9990 chunk 187 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 432 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 434 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 359 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 HIS ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** H 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.051869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.036650 restraints weight = 298493.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.037848 restraints weight = 166159.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.038649 restraints weight = 110718.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.039191 restraints weight = 82796.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.039551 restraints weight = 67091.275| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 36051 Z= 0.142 Angle : 0.648 11.421 49215 Z= 0.327 Chirality : 0.045 0.325 5766 Planarity : 0.004 0.047 6204 Dihedral : 5.680 56.183 6354 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.96 % Rotamer: Outliers : 1.68 % Allowed : 13.49 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: -0.10 (0.13), residues: 4353 helix: 0.99 (0.20), residues: 702 sheet: -0.13 (0.14), residues: 1311 loop : -0.26 (0.14), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 231 TYR 0.026 0.002 TYR A1110 PHE 0.030 0.002 PHE B 823 TRP 0.024 0.002 TRP A 104 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00317 (35916) covalent geometry : angle 0.63214 (48867) SS BOND : bond 0.00350 ( 57) SS BOND : angle 0.87678 ( 114) hydrogen bonds : bond 0.04164 ( 1430) hydrogen bonds : angle 6.26400 ( 3897) link_BETA1-4 : bond 0.00537 ( 33) link_BETA1-4 : angle 1.74427 ( 99) link_NAG-ASN : bond 0.00471 ( 45) link_NAG-ASN : angle 2.40476 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 226 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9319 (mt) REVERT: A 309 GLU cc_start: 0.9093 (pm20) cc_final: 0.8765 (pm20) REVERT: A 759 PHE cc_start: 0.8752 (t80) cc_final: 0.8220 (t80) REVERT: A 780 GLU cc_start: 0.8992 (tp30) cc_final: 0.8743 (tt0) REVERT: A 936 ASP cc_start: 0.9197 (m-30) cc_final: 0.8864 (t0) REVERT: A 954 GLN cc_start: 0.9348 (mt0) cc_final: 0.9130 (pt0) REVERT: A 1001 LEU cc_start: 0.9785 (tt) cc_final: 0.9548 (pp) REVERT: A 1038 LYS cc_start: 0.9441 (mttp) cc_final: 0.9061 (ptmt) REVERT: A 1123 SER cc_start: 0.8395 (t) cc_final: 0.8066 (t) REVERT: A 1125 ASN cc_start: 0.8483 (t0) cc_final: 0.8160 (t0) REVERT: B 104 TRP cc_start: 0.8640 (m-90) cc_final: 0.8408 (m-90) REVERT: B 776 LYS cc_start: 0.9436 (tmtt) cc_final: 0.8921 (tptp) REVERT: B 780 GLU cc_start: 0.9117 (tp30) cc_final: 0.8668 (tp30) REVERT: B 796 ASP cc_start: 0.8791 (m-30) cc_final: 0.8508 (p0) REVERT: B 936 ASP cc_start: 0.9200 (m-30) cc_final: 0.8892 (t0) REVERT: B 954 GLN cc_start: 0.9400 (mt0) cc_final: 0.9082 (pt0) REVERT: B 1001 LEU cc_start: 0.9816 (OUTLIER) cc_final: 0.9498 (pp) REVERT: B 1038 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.8320 (ptpp) REVERT: B 1123 SER cc_start: 0.8343 (t) cc_final: 0.8021 (t) REVERT: B 1125 ASN cc_start: 0.8319 (t0) cc_final: 0.7956 (t0) REVERT: C 104 TRP cc_start: 0.8583 (m-90) cc_final: 0.8367 (m-90) REVERT: C 135 PHE cc_start: 0.8241 (t80) cc_final: 0.7936 (t80) REVERT: C 226 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9328 (mt) REVERT: C 773 GLU cc_start: 0.9260 (tt0) cc_final: 0.7875 (tm-30) REVERT: C 786 LYS cc_start: 0.9023 (OUTLIER) cc_final: 0.8795 (pttt) REVERT: C 796 ASP cc_start: 0.8723 (m-30) cc_final: 0.8515 (p0) REVERT: C 869 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.8814 (ptp) REVERT: C 936 ASP cc_start: 0.9165 (m-30) cc_final: 0.8839 (t0) REVERT: C 954 GLN cc_start: 0.9370 (mt0) cc_final: 0.9109 (pt0) REVERT: C 1001 LEU cc_start: 0.9822 (tp) cc_final: 0.9454 (pp) REVERT: C 1002 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8431 (tm-30) REVERT: C 1017 GLU cc_start: 0.9044 (tm-30) cc_final: 0.8832 (pp20) REVERT: C 1031 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8495 (mm-30) REVERT: C 1123 SER cc_start: 0.8237 (t) cc_final: 0.7970 (t) REVERT: C 1125 ASN cc_start: 0.8412 (t0) cc_final: 0.8077 (t0) REVERT: L 4 MET cc_start: 0.7870 (mmm) cc_final: 0.7092 (tpp) REVERT: L 11 LEU cc_start: 0.9197 (tp) cc_final: 0.8822 (pt) REVERT: L 162 ARG cc_start: 0.9124 (tpt90) cc_final: 0.8622 (tpp80) REVERT: H 39 MET cc_start: 0.5419 (mpp) cc_final: 0.4577 (mmm) REVERT: H 84 LYS cc_start: 0.8539 (tptp) cc_final: 0.7787 (ptmt) REVERT: H 115 MET cc_start: 0.7395 (mmm) cc_final: 0.6900 (tpp) REVERT: H 159 ASP cc_start: 0.9504 (m-30) cc_final: 0.9070 (p0) REVERT: M 4 MET cc_start: 0.7464 (mmm) cc_final: 0.6630 (tpp) REVERT: M 11 LEU cc_start: 0.9113 (tp) cc_final: 0.8762 (pt) REVERT: M 162 ARG cc_start: 0.9113 (tpt90) cc_final: 0.8623 (tpp80) REVERT: I 39 MET cc_start: 0.5640 (mpp) cc_final: 0.4588 (mmm) REVERT: I 115 MET cc_start: 0.7136 (tpp) cc_final: 0.6494 (tpp) REVERT: I 159 ASP cc_start: 0.9512 (m-30) cc_final: 0.9158 (p0) REVERT: I 225 LYS cc_start: 0.9491 (tmmt) cc_final: 0.9240 (tppt) REVERT: N 4 MET cc_start: 0.7008 (mmm) cc_final: 0.6167 (tpp) REVERT: N 11 LEU cc_start: 0.9232 (tp) cc_final: 0.8877 (pt) REVERT: N 162 ARG cc_start: 0.9101 (tpt90) cc_final: 0.8618 (tpp80) REVERT: J 91 MET cc_start: 0.7016 (mpp) cc_final: 0.6612 (mpp) REVERT: J 115 MET cc_start: 0.8436 (mmm) cc_final: 0.8146 (mmt) REVERT: J 159 ASP cc_start: 0.9532 (m-30) cc_final: 0.9139 (p0) outliers start: 64 outliers final: 49 residues processed: 257 average time/residue: 0.2507 time to fit residues: 101.7941 Evaluate side-chains 240 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1061 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1038 LYS Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain C residue 1121 PHE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain I residue 221 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 188 optimal weight: 1.9990 chunk 362 optimal weight: 0.6980 chunk 346 optimal weight: 30.0000 chunk 350 optimal weight: 7.9990 chunk 339 optimal weight: 20.0000 chunk 168 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 376 optimal weight: 8.9990 chunk 209 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 394 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.051298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.036044 restraints weight = 302954.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.037239 restraints weight = 169572.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.038037 restraints weight = 113242.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.038572 restraints weight = 84878.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.038928 restraints weight = 69034.605| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.6766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 36051 Z= 0.169 Angle : 0.664 19.230 49215 Z= 0.331 Chirality : 0.045 0.328 5766 Planarity : 0.004 0.047 6204 Dihedral : 5.608 56.818 6354 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 1.49 % Allowed : 14.04 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: -0.09 (0.13), residues: 4353 helix: 0.86 (0.20), residues: 708 sheet: -0.00 (0.14), residues: 1272 loop : -0.29 (0.13), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C1019 TYR 0.029 0.002 TYR A1110 PHE 0.024 0.002 PHE B1042 TRP 0.020 0.002 TRP A 104 HIS 0.007 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00375 (35916) covalent geometry : angle 0.64684 (48867) SS BOND : bond 0.00381 ( 57) SS BOND : angle 0.91281 ( 114) hydrogen bonds : bond 0.04238 ( 1430) hydrogen bonds : angle 6.24495 ( 3897) link_BETA1-4 : bond 0.00503 ( 33) link_BETA1-4 : angle 1.75333 ( 99) link_NAG-ASN : bond 0.00454 ( 45) link_NAG-ASN : angle 2.50583 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8706 Ramachandran restraints generated. 4353 Oldfield, 0 Emsley, 4353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 192 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 226 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9340 (mt) REVERT: A 309 GLU cc_start: 0.9141 (pm20) cc_final: 0.8805 (pm20) REVERT: A 759 PHE cc_start: 0.8804 (t80) cc_final: 0.8264 (t80) REVERT: A 780 GLU cc_start: 0.9045 (tp30) cc_final: 0.8830 (tt0) REVERT: A 936 ASP cc_start: 0.9233 (m-30) cc_final: 0.8957 (t0) REVERT: A 954 GLN cc_start: 0.9398 (mt0) cc_final: 0.9153 (pt0) REVERT: A 1001 LEU cc_start: 0.9790 (tt) cc_final: 0.9555 (pp) REVERT: A 1123 SER cc_start: 0.8399 (t) cc_final: 0.8086 (t) REVERT: A 1125 ASN cc_start: 0.8425 (t0) cc_final: 0.8083 (t0) REVERT: B 104 TRP cc_start: 0.8673 (m-90) cc_final: 0.8447 (m-90) REVERT: B 776 LYS cc_start: 0.9456 (tmtt) cc_final: 0.8912 (tptp) REVERT: B 780 GLU cc_start: 0.9166 (tp30) cc_final: 0.8780 (tp30) REVERT: B 796 ASP cc_start: 0.8851 (m-30) cc_final: 0.8523 (p0) REVERT: B 936 ASP cc_start: 0.9225 (m-30) cc_final: 0.8921 (t0) REVERT: B 1001 LEU cc_start: 0.9825 (OUTLIER) cc_final: 0.9507 (pp) REVERT: B 1123 SER cc_start: 0.8338 (t) cc_final: 0.8020 (t) REVERT: B 1125 ASN cc_start: 0.8281 (t0) cc_final: 0.7901 (t0) REVERT: C 104 TRP cc_start: 0.8631 (m-90) cc_final: 0.8408 (m-90) REVERT: C 135 PHE cc_start: 0.8362 (t80) cc_final: 0.8047 (t80) REVERT: C 226 LEU cc_start: 0.9652 (OUTLIER) cc_final: 0.9351 (mt) REVERT: C 786 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8853 (pttt) REVERT: C 796 ASP cc_start: 0.8799 (m-30) cc_final: 0.8533 (p0) REVERT: C 869 MET cc_start: 0.9324 (OUTLIER) cc_final: 0.8861 (ptp) REVERT: C 936 ASP cc_start: 0.9207 (m-30) cc_final: 0.8881 (t0) REVERT: C 954 GLN cc_start: 0.9416 (mt0) cc_final: 0.9168 (pt0) REVERT: C 1001 LEU cc_start: 0.9815 (tp) cc_final: 0.9518 (pp) REVERT: C 1017 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8842 (pp20) REVERT: C 1031 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8592 (mm-30) REVERT: C 1123 SER cc_start: 0.8216 (t) cc_final: 0.7962 (t) REVERT: C 1125 ASN cc_start: 0.8378 (t0) cc_final: 0.8045 (t0) REVERT: L 4 MET cc_start: 0.8001 (mmm) cc_final: 0.7160 (tpp) REVERT: L 11 LEU cc_start: 0.9206 (tp) cc_final: 0.8800 (pt) REVERT: L 162 ARG cc_start: 0.9155 (tpt90) cc_final: 0.8626 (tpp80) REVERT: H 39 MET cc_start: 0.5421 (mpp) cc_final: 0.4628 (mmm) REVERT: H 84 LYS cc_start: 0.8623 (tptp) cc_final: 0.7896 (ptmt) REVERT: H 115 MET cc_start: 0.7432 (mmm) cc_final: 0.6880 (tpp) REVERT: H 159 ASP cc_start: 0.9513 (m-30) cc_final: 0.9095 (p0) REVERT: M 4 MET cc_start: 0.7330 (mmm) cc_final: 0.6533 (tpp) REVERT: M 11 LEU cc_start: 0.9139 (tp) cc_final: 0.8772 (pt) REVERT: M 162 ARG cc_start: 0.9173 (tpt90) cc_final: 0.8700 (tpp80) REVERT: I 39 MET cc_start: 0.5611 (mpp) cc_final: 0.4582 (mmm) REVERT: I 115 MET cc_start: 0.7144 (tpp) cc_final: 0.6474 (tpp) REVERT: I 159 ASP cc_start: 0.9519 (m-30) cc_final: 0.9171 (p0) REVERT: I 225 LYS cc_start: 0.9506 (tmmt) cc_final: 0.9268 (tppt) REVERT: N 4 MET cc_start: 0.7187 (mmm) cc_final: 0.6392 (tpp) REVERT: N 11 LEU cc_start: 0.9247 (tp) cc_final: 0.8876 (pt) REVERT: N 162 ARG cc_start: 0.9149 (tpt90) cc_final: 0.8689 (tpp80) REVERT: J 91 MET cc_start: 0.7016 (mpp) cc_final: 0.6620 (mpp) REVERT: J 115 MET cc_start: 0.8476 (mmm) cc_final: 0.8212 (mmt) REVERT: J 159 ASP cc_start: 0.9546 (m-30) cc_final: 0.9164 (p0) outliers start: 57 outliers final: 48 residues processed: 239 average time/residue: 0.2503 time to fit residues: 93.8298 Evaluate side-chains 240 residues out of total 3819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 187 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 436 TRP Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 562 PHE Chi-restraints excluded: chain A residue 695 TYR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 562 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 674 TYR Chi-restraints excluded: chain B residue 695 TYR Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1041 ASP Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1121 PHE Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 386 LYS Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 674 TYR Chi-restraints excluded: chain C residue 695 TYR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1061 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 196 VAL Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain M residue 2 ILE Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 LEU Chi-restraints excluded: chain I residue 196 VAL Chi-restraints excluded: chain I residue 210 ILE Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 12 LEU Chi-restraints excluded: chain J residue 196 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 42 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 340 optimal weight: 0.8980 chunk 282 optimal weight: 4.9990 chunk 388 optimal weight: 30.0000 chunk 171 optimal weight: 2.9990 chunk 302 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 208 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** H 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.050608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.035435 restraints weight = 307558.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.036623 restraints weight = 170415.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.037405 restraints weight = 113360.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.037929 restraints weight = 84945.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.038280 restraints weight = 69103.356| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.7027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 36051 Z= 0.205 Angle : 0.680 15.051 49215 Z= 0.341 Chirality : 0.045 0.312 5766 Planarity : 0.005 0.046 6204 Dihedral : 5.704 57.048 6354 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.64 % Favored : 95.29 % Rotamer: Outliers : 1.70 % Allowed : 13.93 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.49 % 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: -0.12 (0.13), residues: 4353 helix: 0.99 (0.20), residues: 705 sheet: -0.01 (0.14), residues: 1290 loop : -0.37 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG A1091 TYR 0.023 0.002 TYR A1047 PHE 0.026 0.002 PHE A1121 TRP 0.018 0.002 TRP A 104 HIS 0.007 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00442 (35916) covalent geometry : angle 0.66237 (48867) SS BOND : bond 0.00436 ( 57) SS BOND : angle 0.94008 ( 114) hydrogen bonds : bond 0.04355 ( 1430) hydrogen bonds : angle 6.30521 ( 3897) link_BETA1-4 : bond 0.00523 ( 33) link_BETA1-4 : angle 1.80343 ( 99) link_NAG-ASN : bond 0.00494 ( 45) link_NAG-ASN : angle 2.60201 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7404.64 seconds wall clock time: 129 minutes 8.30 seconds (7748.30 seconds total)