Starting phenix.real_space_refine on Sat Mar 7 00:13:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wuh_32832/03_2026/7wuh_32832.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wuh_32832/03_2026/7wuh_32832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wuh_32832/03_2026/7wuh_32832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wuh_32832/03_2026/7wuh_32832.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wuh_32832/03_2026/7wuh_32832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wuh_32832/03_2026/7wuh_32832.map" } resolution = 4.7 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= -0.005 sd= 0.385 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 144 5.16 5 C 22517 2.51 5 N 5779 2.21 5 O 7129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 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: 35569 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 8062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8062 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 49, 'TRANS': 988} Chain breaks: 6 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 8072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8072 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 48, 'TRANS': 989} Chain breaks: 5 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "E" Number of atoms: 8123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1044, 8123 Classifications: {'peptide': 1044} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 51, 'TRANS': 992} Chain breaks: 7 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain: "F" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1705 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 209} Chain: "H" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain: "I" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1705 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 209} Chain: "K" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 206} Chain: "L" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1705 Classifications: {'peptide': 219} Link IDs: {'PCIS': 3, 'PTRANS': 6, 'TRANS': 209} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 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: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" 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: "a" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "b" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "c" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} 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: "g" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "E" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.98, per 1000 atoms: 0.22 Number of scatterers: 35569 At special positions: 0 Unit cell: (161.02, 151.06, 231.57, 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 144 16.00 O 7129 8.00 N 5779 7.00 C 22517 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.98 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.04 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 146 " - pdb=" SG CYS D 202 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 200 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 94 " distance=2.03 Simple disulfide: pdb=" SG CYS I 140 " - pdb=" SG CYS I 200 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 146 " - pdb=" SG CYS K 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA W 3 " - " MAN W 4 " " BMA d 3 " - " MAN d 4 " " BMA f 3 " - " MAN f 4 " " MAN f 4 " - " MAN f 5 " ALPHA1-6 " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " " BMA W 3 " - " MAN W 5 " " BMA Y 3 " - " MAN Y 4 " " MAN d 4 " - " MAN d 6 " " MAN f 4 " - " MAN f 6 " BETA1-2 " MAN d 4 " - " NAG d 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 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 f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG a 1 " - " FUC a 4 " " NAG b 1 " - " FUC b 3 " " NAG c 1 " - " FUC c 2 " " NAG g 1 " - " FUC g 4 " NAG-ASN " NAG A1301 " - " ASN A 657 " " NAG A1302 " - " ASN A 709 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 61 " " NAG A1305 " - " ASN A 616 " " NAG B 1 " - " ASN A 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 74 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C1074 " " NAG C1308 " - " ASN C1098 " " NAG E1301 " - " ASN E1098 " " NAG E1302 " - " ASN E 61 " " NAG E1303 " - " ASN E 165 " " NAG E1304 " - " ASN E 122 " " NAG E1305 " - " ASN E 234 " " NAG G 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 282 " " NAG K 301 " - " ASN K 102 " " NAG M 1 " - " ASN A 331 " " NAG N 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " " NAG P 1 " - " ASN A 122 " " NAG Q 1 " - " ASN A1074 " " NAG R 1 " - " ASN C 149 " " NAG S 1 " - " ASN C 331 " " NAG T 1 " - " ASN C 122 " " NAG U 1 " - " ASN C 165 " " NAG V 1 " - " ASN C 709 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C 282 " " NAG Z 1 " - " ASN E 282 " " NAG a 1 " - " ASN E 717 " " NAG b 1 " - " ASN E 149 " " NAG c 1 " - " ASN E 603 " " NAG d 1 " - " ASN E 331 " " NAG e 1 " - " ASN E 801 " " NAG f 1 " - " ASN E1074 " " NAG g 1 " - " ASN H 102 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.20 Conformation dependent library (CDL) restraints added in 1.4 seconds 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8280 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 67 sheets defined 18.4% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.654A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.920A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.868A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.582A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.244A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (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 902 Processing helix chain 'A' and resid 902 through 910 removed outlier: 3.958A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 940 removed outlier: 3.849A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 968 removed outlier: 3.994A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.589A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 404 through 410 removed outlier: 4.063A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN C 409 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 Processing helix chain 'C' and resid 757 through 783 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 884 through 891 removed outlier: 3.620A pdb=" N THR C 887 " --> pdb=" O SER C 884 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.940A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 939 removed outlier: 4.513A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 944 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 977 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.709A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 365 through 372 removed outlier: 3.773A pdb=" N ALA E 372 " --> pdb=" O TYR E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 removed outlier: 3.591A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'E' and resid 746 through 757 removed outlier: 3.987A pdb=" N GLN E 755 " --> pdb=" O ASN E 751 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR E 756 " --> pdb=" O LEU E 752 " (cutoff:3.500A) Processing helix chain 'E' and resid 757 through 782 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 885 through 891 removed outlier: 3.842A pdb=" N GLY E 889 " --> pdb=" O TRP E 886 " (cutoff:3.500A) Processing helix chain 'E' and resid 897 through 908 removed outlier: 4.097A pdb=" N ALA E 903 " --> pdb=" O ALA E 899 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR E 904 " --> pdb=" O MET E 900 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 940 removed outlier: 7.195A pdb=" N LYS E 921 " --> pdb=" O TYR E 917 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU E 922 " --> pdb=" O GLU E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 942 through 944 No H-bonds generated for 'chain 'E' and resid 942 through 944' Processing helix chain 'E' and resid 945 through 968 removed outlier: 4.010A pdb=" N LEU E 966 " --> pdb=" O LEU E 962 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER E 967 " --> pdb=" O VAL E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 977 through 984 removed outlier: 4.072A pdb=" N LEU E 981 " --> pdb=" O LEU E 977 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU E 984 " --> pdb=" O ILE E 980 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 removed outlier: 3.890A pdb=" N ARG E 995 " --> pdb=" O VAL E 991 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'F' and resid 32 through 36 removed outlier: 4.615A pdb=" N LYS F 36 " --> pdb=" O SER F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.910A pdb=" N LEU F 89 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 188 through 195 removed outlier: 3.702A pdb=" N GLU F 193 " --> pdb=" O LYS F 189 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS F 194 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N HIS F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 160 through 164 Processing helix chain 'I' and resid 85 through 89 removed outlier: 3.526A pdb=" N LEU I 89 " --> pdb=" O ALA I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 132 removed outlier: 3.666A pdb=" N LYS I 132 " --> pdb=" O ASP I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 195 removed outlier: 3.945A pdb=" N TYR I 192 " --> pdb=" O SER I 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.114A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 65 removed outlier: 3.959A pdb=" N LYS K 65 " --> pdb=" O GLN K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'K' and resid 191 through 195 removed outlier: 4.001A pdb=" N LEU K 195 " --> pdb=" O SER K 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 36 removed outlier: 3.510A pdb=" N GLN L 35 " --> pdb=" O SER L 32 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS L 36 " --> pdb=" O SER L 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 32 through 36' Processing helix chain 'L' and resid 128 through 133 removed outlier: 3.520A pdb=" N LYS L 132 " --> pdb=" O GLU L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.518A pdb=" N TYR L 192 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU L 193 " --> pdb=" O LYS L 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 188 through 193' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 removed outlier: 3.860A pdb=" N VAL A 62 " --> pdb=" O THR A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 removed outlier: 4.664A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU A 189 " --> pdb=" O THR A 208 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 120 removed outlier: 3.546A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL A 127 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE A 128 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 204 through 205 removed outlier: 3.720A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.710A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 313 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.814A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 583 through 586 removed outlier: 4.506A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY A 566 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N PHE A 565 " --> pdb=" O PHE E 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 610 through 611 removed outlier: 3.669A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 653 through 654 removed outlier: 7.455A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 727 removed outlier: 3.959A pdb=" N SER A 721 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N THR A1066 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 723 " --> pdb=" O HIS A1064 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N HIS A1064 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A1061 " --> pdb=" O GLN A1054 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A1054 " --> pdb=" O VAL A1061 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 7.197A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1077 through 1078 removed outlier: 3.807A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1088 through 1089 removed outlier: 3.699A pdb=" N PHE A1089 " --> pdb=" O PHE A1121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 90 through 92 removed outlier: 4.308A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.712A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 104 through 107 removed outlier: 3.533A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 118 through 122 removed outlier: 3.546A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL C 127 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ASN C 122 " --> pdb=" O ASN C 125 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN C 125 " --> pdb=" O ASN C 122 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 275 through 279 removed outlier: 4.210A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 313 through 316 removed outlier: 7.284A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 325 through 327 removed outlier: 6.290A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 541 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU C 546 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.637A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU C 513 " --> pdb=" O CYS C 432 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.971A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.938A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 643 through 645 Processing sheet with id=AD1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.442A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 718 through 723 removed outlier: 3.564A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1053 through 1056 Processing sheet with id=AD4, first strand: chain 'C' and resid 1088 through 1089 Processing sheet with id=AD5, first strand: chain 'C' and resid 1094 through 1095 removed outlier: 3.607A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AD7, first strand: chain 'E' and resid 51 through 55 removed outlier: 3.870A pdb=" N THR E 51 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR E 274 " --> pdb=" O ASP E 290 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ASP E 290 " --> pdb=" O THR E 274 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU E 276 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA E 288 " --> pdb=" O LEU E 276 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS E 278 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 84 through 85 removed outlier: 3.698A pdb=" N LEU E 84 " --> pdb=" O PHE E 238 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 189 through 191 Processing sheet with id=AE1, first strand: chain 'E' and resid 195 through 197 removed outlier: 4.344A pdb=" N LYS E 195 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS E 202 " --> pdb=" O LYS E 195 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE E 197 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL E 227 " --> pdb=" O ILE E 203 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 311 through 316 removed outlier: 3.556A pdb=" N GLY E 311 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR E 599 " --> pdb=" O GLY E 311 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL E 597 " --> pdb=" O TYR E 313 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR E 315 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 377 through 380 removed outlier: 4.179A pdb=" N CYS E 432 " --> pdb=" O LEU E 513 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU E 513 " --> pdb=" O CYS E 432 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE E 402 " --> pdb=" O TYR E 508 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 551 through 553 Processing sheet with id=AE5, first strand: chain 'E' and resid 643 through 645 removed outlier: 3.566A pdb=" N LEU E 650 " --> pdb=" O PHE E 643 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 665 through 667 removed outlier: 6.543A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 718 through 720 Processing sheet with id=AE8, first strand: chain 'E' and resid 726 through 727 removed outlier: 3.627A pdb=" N VAL E1060 " --> pdb=" O LEU E 727 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 1077 through 1078 removed outlier: 3.764A pdb=" N PHE E1095 " --> pdb=" O ALA E1078 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN E1106 " --> pdb=" O GLU E1111 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N GLU E1111 " --> pdb=" O GLN E1106 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 34 through 37 removed outlier: 4.307A pdb=" N TYR D 35 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ALA D 97 " --> pdb=" O TYR D 35 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 39 through 40 removed outlier: 3.572A pdb=" N SER D 40 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'F' and resid 6 through 7 removed outlier: 3.622A pdb=" N SER F 7 " --> pdb=" O SER F 22 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N CYS F 23 " --> pdb=" O PHE F 77 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N PHE F 77 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER F 71 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 59 through 60 removed outlier: 4.179A pdb=" N SER F 59 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR F 55 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU F 39 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA F 40 " --> pdb=" O GLN F 95 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR F 42 " --> pdb=" O TYR F 93 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 138 through 140 removed outlier: 3.764A pdb=" N VAL F 138 " --> pdb=" O LEU F 185 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU F 185 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N CYS F 140 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER F 183 " --> pdb=" O CYS F 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 153 through 155 removed outlier: 3.612A pdb=" N GLN F 153 " --> pdb=" O GLU F 201 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS F 155 " --> pdb=" O ALA F 199 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ALA F 199 " --> pdb=" O LYS F 155 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.758A pdb=" N GLN H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS H 23 " --> pdb=" O GLN H 5 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'H' and resid 46 through 51 removed outlier: 5.321A pdb=" N TRP H 47 " --> pdb=" O LYS H 38 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LYS H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 72 through 73 removed outlier: 3.919A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 148 through 151 removed outlier: 4.068A pdb=" N ASP H 150 " --> pdb=" O TYR H 182 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 39 through 40 removed outlier: 3.747A pdb=" N GLN I 95 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 142 through 143 removed outlier: 4.204A pdb=" N LEU I 142 " --> pdb=" O LEU I 181 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU I 181 " --> pdb=" O LEU I 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'K' and resid 46 through 49 removed outlier: 7.234A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 126 through 129 removed outlier: 3.921A pdb=" N SER K 126 " --> pdb=" O LYS K 149 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS K 149 " --> pdb=" O SER K 126 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 159 through 160 removed outlier: 3.559A pdb=" N ASN K 203 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.611A pdb=" N SER L 5 " --> pdb=" O LYS L 24 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS L 24 " --> pdb=" O SER L 5 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.492A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR L 108 " --> pdb=" O TYR L 92 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 39 through 41 removed outlier: 4.222A pdb=" N ALA L 40 " --> pdb=" O GLN L 95 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN L 95 " --> pdb=" O ALA L 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AH2, first strand: chain 'L' and resid 71 through 73 removed outlier: 4.002A pdb=" N SER L 71 " --> pdb=" O THR L 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR L 78 " --> pdb=" O SER L 71 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 140 through 145 removed outlier: 5.401A pdb=" N LEU L 141 " --> pdb=" O SER L 183 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER L 183 " --> pdb=" O LEU L 141 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASN L 143 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU L 181 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.011A pdb=" N GLN L 153 " --> pdb=" O GLU L 201 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU L 201 " --> pdb=" O GLN L 153 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS L 155 " --> pdb=" O ALA L 199 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA L 199 " --> pdb=" O LYS L 155 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 1944 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: 8.76 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6162 1.32 - 1.45: 10368 1.45 - 1.58: 19636 1.58 - 1.71: 1 1.71 - 1.83: 182 Bond restraints: 36349 Sorted by residual: bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.474 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C1 BMA f 3 " pdb=" C2 BMA f 3 " ideal model delta sigma weight residual 1.519 1.581 -0.062 2.00e-02 2.50e+03 9.53e+00 bond pdb=" C ASN C 282 " pdb=" O ASN C 282 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.31e-02 5.83e+03 8.52e+00 ... (remaining 36344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 48471 2.80 - 5.59: 884 5.59 - 8.39: 93 8.39 - 11.19: 6 11.19 - 13.99: 5 Bond angle restraints: 49459 Sorted by residual: angle pdb=" C ARG I 99 " pdb=" N TYR I 100 " pdb=" CA TYR I 100 " ideal model delta sigma weight residual 120.49 130.63 -10.14 1.42e+00 4.96e-01 5.10e+01 angle pdb=" CA ASN C 282 " pdb=" CB ASN C 282 " pdb=" CG ASN C 282 " ideal model delta sigma weight residual 112.60 119.60 -7.00 1.00e+00 1.00e+00 4.90e+01 angle pdb=" CA ARG C 995 " pdb=" CB ARG C 995 " pdb=" CG ARG C 995 " ideal model delta sigma weight residual 114.10 126.15 -12.05 2.00e+00 2.50e-01 3.63e+01 angle pdb=" N ASN C 148 " pdb=" CA ASN C 148 " pdb=" C ASN C 148 " ideal model delta sigma weight residual 110.91 117.86 -6.95 1.17e+00 7.31e-01 3.53e+01 angle pdb=" C SER C 155 " pdb=" CA SER C 155 " pdb=" CB SER C 155 " ideal model delta sigma weight residual 117.23 109.39 7.84 1.36e+00 5.41e-01 3.33e+01 ... (remaining 49454 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.45: 21291 23.45 - 46.90: 1210 46.90 - 70.35: 198 70.35 - 93.80: 123 93.80 - 117.25: 79 Dihedral angle restraints: 22901 sinusoidal: 10003 harmonic: 12898 Sorted by residual: dihedral pdb=" CB CYS E1032 " pdb=" SG CYS E1032 " pdb=" SG CYS E1043 " pdb=" CB CYS E1043 " ideal model delta sinusoidal sigma weight residual 93.00 -176.61 -90.39 1 1.00e+01 1.00e-02 9.67e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 4.24 88.76 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 8.12 84.88 1 1.00e+01 1.00e-02 8.74e+01 ... (remaining 22898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 5819 0.146 - 0.291: 83 0.291 - 0.437: 11 0.437 - 0.583: 3 0.583 - 0.728: 3 Chirality restraints: 5919 Sorted by residual: chirality pdb=" C1 BMA Y 3 " pdb=" O4 NAG Y 2 " pdb=" C2 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-02 2.50e+03 9.22e+02 chirality pdb=" C1 MAN U 4 " pdb=" O6 BMA U 3 " pdb=" C2 MAN U 4 " pdb=" O5 MAN U 4 " both_signs ideal model delta sigma weight residual False 2.40 1.94 0.46 2.00e-02 2.50e+03 5.21e+02 chirality pdb=" C1 MAN Y 4 " pdb=" O6 BMA Y 3 " pdb=" C2 MAN Y 4 " pdb=" O5 MAN Y 4 " both_signs ideal model delta sigma weight residual False 2.40 2.17 0.23 2.00e-02 2.50e+03 1.31e+02 ... (remaining 5916 not shown) Planarity restraints: 6254 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG Y 2 " -0.296 2.00e-02 2.50e+03 2.61e-01 8.50e+02 pdb=" C7 NAG Y 2 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG Y 2 " -0.064 2.00e-02 2.50e+03 pdb=" N2 NAG Y 2 " 0.467 2.00e-02 2.50e+03 pdb=" O7 NAG Y 2 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " 0.298 2.00e-02 2.50e+03 2.50e-01 7.83e+02 pdb=" C7 NAG A1305 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1304 " -0.278 2.00e-02 2.50e+03 2.37e-01 7.00e+02 pdb=" C7 NAG A1304 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG A1304 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG A1304 " 0.411 2.00e-02 2.50e+03 pdb=" O7 NAG A1304 " -0.031 2.00e-02 2.50e+03 ... (remaining 6251 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 767 2.61 - 3.18: 34232 3.18 - 3.76: 56071 3.76 - 4.33: 74856 4.33 - 4.90: 114006 Nonbonded interactions: 279932 Sorted by model distance: nonbonded pdb=" OG1 THR K 24 " pdb=" O SER K 77 " model vdw 2.038 3.040 nonbonded pdb=" O PHE H 105 " pdb=" OH TYR I 42 " model vdw 2.071 3.040 nonbonded pdb=" O ALA E 706 " pdb=" OG SER E 711 " model vdw 2.077 3.040 nonbonded pdb=" O GLU A 309 " pdb=" OH TYR A 313 " model vdw 2.095 3.040 nonbonded pdb=" O ALA C 958 " pdb=" OG1 THR C 961 " model vdw 2.096 3.040 ... (remaining 279927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 69 or resid 78 through 210 or resi \ d 214 through 245 or (resid 265 and (name N or name CA or name C or name O or na \ me CB )) or resid 266 through 621 or resid 641 through 679 or resid 689 through \ 828 or resid 852 or resid 854 through 1134 or resid 1301 through 1305)) selection = (chain 'C' and (resid 26 through 36 or (resid 37 and (name N or name CA or name \ C or name O or name CB )) or resid 38 through 40 or (resid 41 and (name N or nam \ e CA or name C or name O or name CB )) or resid 42 through 69 or resid 78 or (re \ sid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 thro \ ugh 96 or (resid 97 and (name N or name CA or name C or name O or name CB )) or \ resid 98 through 112 or (resid 113 and (name N or name CA or name C or name O or \ name CB )) or resid 114 through 139 or (resid 140 and (name N or name CA or nam \ e C or name O or name CB )) or resid 141 through 152 or (resid 153 through 154 a \ nd (name N or name CA or name C or name O or name CB )) or resid 155 through 167 \ or (resid 168 and (name N or name CA or name C or name O or name CB )) or resid \ 169 through 210 or resid 214 through 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 245 or resid 265 through 5 \ 27 or (resid 528 and (name N or name CA or name C or name O or name CB )) or res \ id 529 through 621 or resid 641 through 679 or resid 689 through 1134 or resid 1 \ 304 through 1308)) selection = (chain 'E' and (resid 26 through 31 or (resid 32 and (name N or name CA or name \ C or name O or name CB )) or resid 33 through 36 or (resid 37 and (name N or nam \ e CA or name C or name O or name CB )) or resid 38 through 40 or (resid 41 and ( \ name N or name CA or name C or name O or name CB )) or resid 42 through 69 or re \ sid 78 or (resid 79 and (name N or name CA or name C or name O or name CB )) or \ resid 80 through 96 or (resid 97 and (name N or name CA or name C or name O or n \ ame CB )) or resid 98 through 112 or (resid 113 and (name N or name CA or name C \ or name O or name CB )) or resid 114 through 139 or (resid 140 and (name N or n \ ame CA or name C or name O or name CB )) or resid 141 through 152 or (resid 153 \ through 154 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 5 through 217 or (resid 218 and (name N or name CA or name C or name O or name C \ B )) or resid 219 through 245 or (resid 265 and (name N or name CA or name C or \ name O or name CB )) or resid 266 through 527 or (resid 528 and (name N or name \ CA or name C or name O or name CB )) or resid 529 through 621 or resid 641 throu \ gh 679 or resid 689 through 828 or resid 831 or resid 854 through 1134 or resid \ 1301 through 1305)) } ncs_group { reference = (chain 'B' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) } ncs_group { reference = chain 'D' selection = chain 'H' selection = (chain 'K' and resid 1 through 218) } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = (chain 'G' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'X' and resid 1) selection = (chain 'c' and resid 1) } ncs_group { reference = (chain 'J' and resid 1 through 3) selection = (chain 'Y' and resid 1 through 3) selection = (chain 'a' and resid 1 through 3) selection = (chain 'g' and resid 1 through 3) } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = (chain 'd' and (resid 1 through 4 or resid 6)) selection = (chain 'f' and (resid 1 through 4 or resid 6)) } 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: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.750 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 31.880 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:1.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 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 : 0.005 0.080 36497 Z= 0.262 Angle : 0.983 19.705 49849 Z= 0.517 Chirality : 0.058 0.728 5919 Planarity : 0.008 0.261 6211 Dihedral : 17.314 117.249 14477 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 27.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.13 % Favored : 87.71 % Rotamer: Outliers : 0.13 % Allowed : 0.47 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % 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: -3.10 (0.12), residues: 4377 helix: -1.21 (0.19), residues: 650 sheet: -1.60 (0.22), residues: 547 loop : -2.52 (0.10), residues: 3180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 995 TYR 0.040 0.002 TYR C 707 PHE 0.050 0.002 PHE C 55 TRP 0.029 0.002 TRP L 41 HIS 0.018 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00511 (36349) covalent geometry : angle 0.93168 (49459) SS BOND : bond 0.00862 ( 48) SS BOND : angle 1.78070 ( 96) hydrogen bonds : bond 0.22848 ( 735) hydrogen bonds : angle 9.56816 ( 1944) Misc. bond : bond 0.00082 ( 2) link_ALPHA1-3 : bond 0.00879 ( 5) link_ALPHA1-3 : angle 2.51558 ( 15) link_ALPHA1-6 : bond 0.00697 ( 8) link_ALPHA1-6 : angle 2.91819 ( 24) link_BETA1-2 : bond 0.00544 ( 1) link_BETA1-2 : angle 1.21681 ( 3) link_BETA1-4 : bond 0.00969 ( 36) link_BETA1-4 : angle 3.53728 ( 108) link_BETA1-6 : bond 0.00619 ( 5) link_BETA1-6 : angle 1.35244 ( 15) link_NAG-ASN : bond 0.01344 ( 43) link_NAG-ASN : angle 5.00467 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 511 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 298 GLU cc_start: 0.8640 (tp30) cc_final: 0.8104 (tp30) REVERT: A 314 GLN cc_start: 0.7739 (tm-30) cc_final: 0.7131 (tm-30) REVERT: A 770 ILE cc_start: 0.9471 (mt) cc_final: 0.9175 (mt) REVERT: A 1005 GLN cc_start: 0.8014 (tp40) cc_final: 0.7661 (tp-100) REVERT: A 1009 THR cc_start: 0.8792 (m) cc_final: 0.8359 (m) REVERT: A 1010 GLN cc_start: 0.7920 (mp10) cc_final: 0.7611 (mp10) REVERT: C 354 ASN cc_start: 0.9545 (t0) cc_final: 0.9252 (t0) REVERT: C 765 ARG cc_start: 0.8423 (tmt-80) cc_final: 0.8042 (ptm-80) REVERT: C 790 LYS cc_start: 0.7854 (mmpt) cc_final: 0.7464 (mmmt) REVERT: C 817 PHE cc_start: 0.8067 (t80) cc_final: 0.7577 (t80) REVERT: C 883 THR cc_start: 0.7548 (p) cc_final: 0.7275 (p) REVERT: C 954 GLN cc_start: 0.8711 (pm20) cc_final: 0.8243 (pm20) REVERT: C 990 GLU cc_start: 0.7821 (tp30) cc_final: 0.7577 (mm-30) REVERT: C 1052 PHE cc_start: 0.8184 (m-10) cc_final: 0.6671 (m-10) REVERT: C 1082 CYS cc_start: 0.8041 (m) cc_final: 0.7741 (m) REVERT: C 1103 PHE cc_start: 0.8262 (m-10) cc_final: 0.8055 (m-80) REVERT: C 1109 PHE cc_start: 0.8988 (t80) cc_final: 0.8496 (t80) REVERT: E 53 ASP cc_start: 0.6752 (t70) cc_final: 0.6369 (t70) REVERT: E 737 ASP cc_start: 0.7464 (p0) cc_final: 0.7057 (p0) REVERT: E 800 PHE cc_start: 0.6994 (m-80) cc_final: 0.6501 (m-80) REVERT: E 925 ASN cc_start: 0.8650 (m110) cc_final: 0.8253 (m-40) REVERT: E 1010 GLN cc_start: 0.7907 (tp-100) cc_final: 0.7590 (tp40) REVERT: E 1121 PHE cc_start: 0.6606 (p90) cc_final: 0.6251 (p90) REVERT: H 47 TRP cc_start: 0.5742 (t60) cc_final: 0.4582 (t60) REVERT: H 81 MET cc_start: -0.1531 (ttp) cc_final: -0.2416 (ttp) REVERT: H 82 GLU cc_start: 0.4124 (pm20) cc_final: 0.3725 (pm20) REVERT: I 92 TYR cc_start: 0.9054 (m-10) cc_final: 0.8709 (m-10) REVERT: L 4 MET cc_start: 0.3641 (mtp) cc_final: 0.0455 (mpp) REVERT: L 42 TYR cc_start: 0.6074 (m-80) cc_final: 0.5083 (m-80) outliers start: 5 outliers final: 2 residues processed: 515 average time/residue: 0.1907 time to fit residues: 165.1188 Evaluate side-chains 412 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 410 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 148 ASN C 321 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 540 ASN C 762 GLN C 856 ASN C 954 GLN C1023 ASN ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 804 GLN ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN F 205 GLN I 130 GLN I 144 ASN K 41 HIS L 44 GLN L 130 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.161353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.126881 restraints weight = 121970.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.130165 restraints weight = 81668.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.132220 restraints weight = 60360.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.133467 restraints weight = 46015.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.134141 restraints weight = 38066.656| |-----------------------------------------------------------------------------| r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 36497 Z= 0.301 Angle : 0.950 19.346 49849 Z= 0.472 Chirality : 0.055 0.467 5919 Planarity : 0.007 0.079 6211 Dihedral : 14.072 100.685 6735 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 28.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.07 % Favored : 86.79 % Rotamer: Outliers : 0.52 % Allowed : 8.65 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % 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: -3.43 (0.11), residues: 4377 helix: -1.58 (0.17), residues: 680 sheet: -1.76 (0.21), residues: 550 loop : -2.74 (0.10), residues: 3147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 577 TYR 0.034 0.003 TYR E 707 PHE 0.025 0.003 PHE E 800 TRP 0.026 0.003 TRP A 436 HIS 0.016 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00622 (36349) covalent geometry : angle 0.90539 (49459) SS BOND : bond 0.00597 ( 48) SS BOND : angle 1.40689 ( 96) hydrogen bonds : bond 0.06971 ( 735) hydrogen bonds : angle 8.07894 ( 1944) Misc. bond : bond 0.00158 ( 2) link_ALPHA1-3 : bond 0.01624 ( 5) link_ALPHA1-3 : angle 3.02561 ( 15) link_ALPHA1-6 : bond 0.00723 ( 8) link_ALPHA1-6 : angle 2.38701 ( 24) link_BETA1-2 : bond 0.00294 ( 1) link_BETA1-2 : angle 0.81934 ( 3) link_BETA1-4 : bond 0.01093 ( 36) link_BETA1-4 : angle 3.29693 ( 108) link_BETA1-6 : bond 0.00719 ( 5) link_BETA1-6 : angle 1.88887 ( 15) link_NAG-ASN : bond 0.00846 ( 43) link_NAG-ASN : angle 4.60095 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 500 time to evaluate : 1.256 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: A 131 CYS cc_start: 0.4600 (OUTLIER) cc_final: 0.3967 (p) REVERT: A 220 PHE cc_start: 0.8124 (p90) cc_final: 0.7803 (p90) REVERT: A 298 GLU cc_start: 0.8770 (tp30) cc_final: 0.8445 (tp30) REVERT: A 314 GLN cc_start: 0.7873 (tm-30) cc_final: 0.7673 (tm-30) REVERT: A 740 MET cc_start: 0.7110 (tpt) cc_final: 0.6796 (tpt) REVERT: A 814 LYS cc_start: 0.7162 (mmtt) cc_final: 0.6930 (mmtt) REVERT: A 993 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7573 (mp) REVERT: A 1005 GLN cc_start: 0.8733 (tp40) cc_final: 0.8198 (tp-100) REVERT: A 1009 THR cc_start: 0.9197 (m) cc_final: 0.8820 (m) REVERT: A 1079 PRO cc_start: 0.7091 (Cg_endo) cc_final: 0.6843 (Cg_exo) REVERT: C 80 ASP cc_start: 0.8416 (t0) cc_final: 0.8089 (t0) REVERT: C 354 ASN cc_start: 0.9480 (t0) cc_final: 0.9047 (t0) REVERT: C 697 MET cc_start: 0.8587 (tmm) cc_final: 0.8366 (tmm) REVERT: C 790 LYS cc_start: 0.8112 (mmpt) cc_final: 0.7745 (mmmt) REVERT: C 817 PHE cc_start: 0.8569 (t80) cc_final: 0.8174 (t80) REVERT: C 900 MET cc_start: 0.3793 (mpp) cc_final: 0.3157 (mpp) REVERT: C 928 ASN cc_start: 0.8766 (m110) cc_final: 0.8540 (m-40) REVERT: C 957 GLN cc_start: 0.8949 (tm-30) cc_final: 0.8644 (tm-30) REVERT: C 995 ARG cc_start: 0.8928 (pmt-80) cc_final: 0.8539 (pmt-80) REVERT: C 996 LEU cc_start: 0.8519 (mm) cc_final: 0.7564 (mm) REVERT: C 1018 ILE cc_start: 0.9345 (mt) cc_final: 0.8833 (mt) REVERT: C 1052 PHE cc_start: 0.8525 (m-10) cc_final: 0.7162 (m-10) REVERT: C 1103 PHE cc_start: 0.8340 (m-10) cc_final: 0.8062 (m-80) REVERT: C 1110 TYR cc_start: 0.8670 (t80) cc_final: 0.8450 (t80) REVERT: E 53 ASP cc_start: 0.6811 (t70) cc_final: 0.6526 (t70) REVERT: E 205 SER cc_start: 0.7174 (p) cc_final: 0.6830 (m) REVERT: E 328 ARG cc_start: 0.7102 (mmm160) cc_final: 0.6732 (mmm160) REVERT: E 737 ASP cc_start: 0.8238 (p0) cc_final: 0.7699 (p0) REVERT: E 800 PHE cc_start: 0.7391 (m-80) cc_final: 0.6682 (m-80) REVERT: E 923 ILE cc_start: 0.9462 (mt) cc_final: 0.9229 (mt) REVERT: E 925 ASN cc_start: 0.8936 (m110) cc_final: 0.8643 (m-40) REVERT: E 926 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8478 (tp-100) REVERT: E 950 ASP cc_start: 0.8340 (m-30) cc_final: 0.7826 (m-30) REVERT: E 957 GLN cc_start: 0.9188 (pp30) cc_final: 0.8934 (pp30) REVERT: E 1007 TYR cc_start: 0.8146 (t80) cc_final: 0.7426 (t80) REVERT: D 11 MET cc_start: 0.6660 (mmp) cc_final: 0.6438 (mmt) REVERT: H 47 TRP cc_start: 0.6052 (t60) cc_final: 0.4819 (t60) REVERT: H 81 MET cc_start: -0.0832 (ttp) cc_final: -0.1376 (ttp) REVERT: K 101 TYR cc_start: 0.7446 (p90) cc_final: 0.7082 (p90) REVERT: L 4 MET cc_start: 0.4149 (mtp) cc_final: 0.0892 (mpp) REVERT: L 42 TYR cc_start: 0.6591 (m-80) cc_final: 0.6357 (m-80) REVERT: L 109 LYS cc_start: 0.6902 (tttt) cc_final: 0.6241 (tptt) outliers start: 20 outliers final: 7 residues processed: 517 average time/residue: 0.1923 time to fit residues: 167.1359 Evaluate side-chains 413 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 403 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 189 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 246 optimal weight: 20.0000 chunk 156 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 262 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 856 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN C1023 ASN ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E 955 ASN ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN L 95 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.166370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.131570 restraints weight = 124823.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.134082 restraints weight = 85288.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.136411 restraints weight = 61819.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.138194 restraints weight = 48429.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.138992 restraints weight = 40125.200| |-----------------------------------------------------------------------------| r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 36497 Z= 0.188 Angle : 0.829 19.435 49849 Z= 0.406 Chirality : 0.052 0.419 5919 Planarity : 0.006 0.085 6211 Dihedral : 12.625 101.212 6735 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 22.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.51 % Favored : 88.37 % Rotamer: Outliers : 0.16 % Allowed : 4.61 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % 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: -3.25 (0.11), residues: 4377 helix: -1.28 (0.18), residues: 677 sheet: -1.75 (0.21), residues: 559 loop : -2.64 (0.10), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 34 TYR 0.033 0.002 TYR E 707 PHE 0.023 0.002 PHE C 65 TRP 0.019 0.002 TRP C 436 HIS 0.012 0.002 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00399 (36349) covalent geometry : angle 0.78537 (49459) SS BOND : bond 0.00422 ( 48) SS BOND : angle 1.28178 ( 96) hydrogen bonds : bond 0.06099 ( 735) hydrogen bonds : angle 7.63172 ( 1944) Misc. bond : bond 0.00082 ( 2) link_ALPHA1-3 : bond 0.01622 ( 5) link_ALPHA1-3 : angle 2.46182 ( 15) link_ALPHA1-6 : bond 0.00649 ( 8) link_ALPHA1-6 : angle 2.10621 ( 24) link_BETA1-2 : bond 0.00635 ( 1) link_BETA1-2 : angle 0.51143 ( 3) link_BETA1-4 : bond 0.00881 ( 36) link_BETA1-4 : angle 3.00589 ( 108) link_BETA1-6 : bond 0.00819 ( 5) link_BETA1-6 : angle 1.63243 ( 15) link_NAG-ASN : bond 0.00698 ( 43) link_NAG-ASN : angle 4.32135 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 545 time to evaluate : 1.272 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: A 220 PHE cc_start: 0.8012 (p90) cc_final: 0.7755 (p90) REVERT: A 298 GLU cc_start: 0.8667 (tp30) cc_final: 0.8309 (tp30) REVERT: A 312 ILE cc_start: 0.8882 (pt) cc_final: 0.8650 (pt) REVERT: A 314 GLN cc_start: 0.7832 (tm-30) cc_final: 0.7288 (tm-30) REVERT: A 727 LEU cc_start: 0.8805 (mt) cc_final: 0.8592 (mt) REVERT: A 817 PHE cc_start: 0.8076 (t80) cc_final: 0.7822 (t80) REVERT: A 993 ILE cc_start: 0.7795 (OUTLIER) cc_final: 0.7499 (mt) REVERT: A 1005 GLN cc_start: 0.8380 (tp40) cc_final: 0.7898 (tp-100) REVERT: C 53 ASP cc_start: 0.7881 (t70) cc_final: 0.7336 (t70) REVERT: C 80 ASP cc_start: 0.8438 (t0) cc_final: 0.8003 (t0) REVERT: C 314 GLN cc_start: 0.8684 (tp40) cc_final: 0.8317 (tt0) REVERT: C 354 ASN cc_start: 0.9501 (t0) cc_final: 0.9191 (t0) REVERT: C 790 LYS cc_start: 0.7906 (mmpt) cc_final: 0.7538 (mmmt) REVERT: C 808 ASP cc_start: 0.9061 (t70) cc_final: 0.8858 (t0) REVERT: C 817 PHE cc_start: 0.8285 (t80) cc_final: 0.7831 (t80) REVERT: C 901 GLN cc_start: 0.8579 (pp30) cc_final: 0.8258 (pp30) REVERT: C 996 LEU cc_start: 0.8398 (mm) cc_final: 0.8086 (mm) REVERT: C 1018 ILE cc_start: 0.9236 (mt) cc_final: 0.8643 (mt) REVERT: C 1050 MET cc_start: 0.7242 (ttt) cc_final: 0.6882 (ttt) REVERT: C 1052 PHE cc_start: 0.8359 (m-10) cc_final: 0.6808 (m-10) REVERT: C 1103 PHE cc_start: 0.8225 (m-10) cc_final: 0.7967 (m-80) REVERT: E 53 ASP cc_start: 0.6806 (t70) cc_final: 0.6493 (t70) REVERT: E 205 SER cc_start: 0.7205 (p) cc_final: 0.6744 (m) REVERT: E 328 ARG cc_start: 0.7064 (mmm160) cc_final: 0.6747 (mmm160) REVERT: E 737 ASP cc_start: 0.8062 (p0) cc_final: 0.7533 (p0) REVERT: E 800 PHE cc_start: 0.7218 (m-80) cc_final: 0.6555 (m-80) REVERT: E 925 ASN cc_start: 0.8862 (m110) cc_final: 0.8459 (m-40) REVERT: E 950 ASP cc_start: 0.8199 (m-30) cc_final: 0.7660 (m-30) REVERT: E 1007 TYR cc_start: 0.7822 (t80) cc_final: 0.7023 (t80) REVERT: E 1010 GLN cc_start: 0.8087 (tp40) cc_final: 0.7781 (tp-100) REVERT: E 1121 PHE cc_start: 0.6520 (p90) cc_final: 0.6144 (p90) REVERT: H 47 TRP cc_start: 0.5846 (t60) cc_final: 0.4934 (t60) REVERT: K 101 TYR cc_start: 0.7217 (p90) cc_final: 0.7016 (p90) REVERT: L 4 MET cc_start: 0.4807 (mtp) cc_final: 0.1484 (mpp) REVERT: L 109 LYS cc_start: 0.6751 (tttt) cc_final: 0.6427 (ptmt) outliers start: 6 outliers final: 1 residues processed: 549 average time/residue: 0.1940 time to fit residues: 177.8993 Evaluate side-chains 425 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 423 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 221 optimal weight: 9.9990 chunk 285 optimal weight: 2.9990 chunk 133 optimal weight: 0.1980 chunk 365 optimal weight: 50.0000 chunk 431 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 407 optimal weight: 50.0000 chunk 186 optimal weight: 1.9990 chunk 234 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 434 optimal weight: 0.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN C 540 ASN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 856 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E 955 ASN ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 GLN ** L 95 GLN ** 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 = 0.4444 r_free = 0.4444 target = 0.168478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.133917 restraints weight = 123579.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.136944 restraints weight = 81773.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.139316 restraints weight = 58829.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.140956 restraints weight = 45910.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.141799 restraints weight = 38424.965| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6607 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 36497 Z= 0.156 Angle : 0.792 19.648 49849 Z= 0.385 Chirality : 0.051 0.416 5919 Planarity : 0.006 0.083 6211 Dihedral : 11.344 95.943 6735 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.01 % Favored : 88.87 % Rotamer: Outliers : 0.16 % Allowed : 3.93 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.12), residues: 4377 helix: -1.19 (0.18), residues: 686 sheet: -1.73 (0.21), residues: 568 loop : -2.56 (0.10), residues: 3123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 99 TYR 0.027 0.002 TYR A 873 PHE 0.026 0.002 PHE H 29 TRP 0.020 0.002 TRP L 154 HIS 0.010 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00329 (36349) covalent geometry : angle 0.74889 (49459) SS BOND : bond 0.00413 ( 48) SS BOND : angle 1.10034 ( 96) hydrogen bonds : bond 0.05314 ( 735) hydrogen bonds : angle 7.31821 ( 1944) Misc. bond : bond 0.00074 ( 2) link_ALPHA1-3 : bond 0.01700 ( 5) link_ALPHA1-3 : angle 2.38284 ( 15) link_ALPHA1-6 : bond 0.00591 ( 8) link_ALPHA1-6 : angle 2.01468 ( 24) link_BETA1-2 : bond 0.00567 ( 1) link_BETA1-2 : angle 0.44005 ( 3) link_BETA1-4 : bond 0.00869 ( 36) link_BETA1-4 : angle 2.88296 ( 108) link_BETA1-6 : bond 0.00852 ( 5) link_BETA1-6 : angle 1.66045 ( 15) link_NAG-ASN : bond 0.00660 ( 43) link_NAG-ASN : angle 4.22519 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 535 time to evaluate : 1.274 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: A 131 CYS cc_start: 0.4669 (OUTLIER) cc_final: 0.4068 (p) REVERT: A 220 PHE cc_start: 0.8043 (p90) cc_final: 0.7759 (p90) REVERT: A 298 GLU cc_start: 0.8626 (tp30) cc_final: 0.8328 (tp30) REVERT: A 314 GLN cc_start: 0.7800 (tm-30) cc_final: 0.7222 (tm-30) REVERT: A 953 ASN cc_start: 0.8087 (m110) cc_final: 0.7777 (m110) REVERT: A 1028 LYS cc_start: 0.9573 (mttt) cc_final: 0.9370 (mttm) REVERT: A 1064 HIS cc_start: 0.8238 (m170) cc_final: 0.7784 (m170) REVERT: C 44 ARG cc_start: 0.8666 (ptt-90) cc_final: 0.8076 (ptt180) REVERT: C 80 ASP cc_start: 0.8376 (t0) cc_final: 0.7920 (t0) REVERT: C 354 ASN cc_start: 0.9466 (t0) cc_final: 0.9191 (t0) REVERT: C 396 TYR cc_start: 0.8584 (m-80) cc_final: 0.8085 (m-80) REVERT: C 790 LYS cc_start: 0.7857 (mmpt) cc_final: 0.7562 (mmmt) REVERT: C 817 PHE cc_start: 0.8234 (t80) cc_final: 0.7883 (t80) REVERT: C 900 MET cc_start: 0.3844 (mpp) cc_final: 0.3252 (mpp) REVERT: C 996 LEU cc_start: 0.8354 (mm) cc_final: 0.8138 (mm) REVERT: C 1018 ILE cc_start: 0.9287 (mt) cc_final: 0.8684 (mt) REVERT: C 1052 PHE cc_start: 0.8446 (m-10) cc_final: 0.7390 (m-10) REVERT: C 1103 PHE cc_start: 0.8215 (m-10) cc_final: 0.7945 (m-80) REVERT: C 1110 TYR cc_start: 0.8550 (t80) cc_final: 0.8348 (t80) REVERT: C 1114 ILE cc_start: 0.8102 (mm) cc_final: 0.7729 (tp) REVERT: E 53 ASP cc_start: 0.6990 (t70) cc_final: 0.6656 (t70) REVERT: E 205 SER cc_start: 0.7122 (p) cc_final: 0.6604 (m) REVERT: E 328 ARG cc_start: 0.7085 (mmm160) cc_final: 0.6805 (mmm160) REVERT: E 737 ASP cc_start: 0.8039 (p0) cc_final: 0.7488 (p0) REVERT: E 775 ASP cc_start: 0.8592 (p0) cc_final: 0.8314 (p0) REVERT: E 780 GLU cc_start: 0.7704 (mp0) cc_final: 0.7373 (tp30) REVERT: E 784 GLN cc_start: 0.7425 (tm-30) cc_final: 0.7078 (tm-30) REVERT: E 800 PHE cc_start: 0.7114 (m-80) cc_final: 0.6467 (m-80) REVERT: E 873 TYR cc_start: 0.8543 (m-80) cc_final: 0.8323 (m-80) REVERT: E 925 ASN cc_start: 0.8918 (m110) cc_final: 0.8491 (m-40) REVERT: E 950 ASP cc_start: 0.8295 (m-30) cc_final: 0.7723 (m-30) REVERT: E 962 LEU cc_start: 0.9283 (tp) cc_final: 0.9076 (tp) REVERT: E 1007 TYR cc_start: 0.7895 (t80) cc_final: 0.7119 (t80) REVERT: E 1010 GLN cc_start: 0.8140 (tp40) cc_final: 0.7779 (tp-100) REVERT: E 1050 MET cc_start: 0.7855 (ppp) cc_final: 0.7574 (ppp) REVERT: E 1121 PHE cc_start: 0.6351 (p90) cc_final: 0.5922 (p90) REVERT: H 47 TRP cc_start: 0.5969 (t60) cc_final: 0.5042 (t60) REVERT: K 81 MET cc_start: 0.4164 (tpt) cc_final: 0.3217 (tpt) REVERT: K 82 GLU cc_start: 0.5929 (pt0) cc_final: 0.5586 (pt0) REVERT: L 4 MET cc_start: 0.4948 (mtp) cc_final: 0.2031 (mpp) REVERT: L 42 TYR cc_start: 0.5777 (m-80) cc_final: 0.5238 (m-80) REVERT: L 109 LYS cc_start: 0.6686 (tttt) cc_final: 0.6411 (ptmt) outliers start: 6 outliers final: 0 residues processed: 540 average time/residue: 0.1931 time to fit residues: 174.8035 Evaluate side-chains 421 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 420 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 423 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 228 optimal weight: 20.0000 chunk 412 optimal weight: 1.9990 chunk 32 optimal weight: 0.0870 chunk 362 optimal weight: 7.9990 chunk 371 optimal weight: 0.0470 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 250 optimal weight: 20.0000 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 ASN A 901 GLN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 856 ASN C 901 GLN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS E 121 ASN E 134 GLN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 439 ASN ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN E 777 ASN ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E 955 ASN ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN F 37 ASN F 96 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.170730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.137033 restraints weight = 120443.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.140652 restraints weight = 78563.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.141954 restraints weight = 59254.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.143849 restraints weight = 44779.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.144823 restraints weight = 36336.384| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6466 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36497 Z= 0.137 Angle : 0.766 19.717 49849 Z= 0.372 Chirality : 0.051 0.414 5919 Planarity : 0.005 0.087 6211 Dihedral : 10.219 87.820 6735 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.08 % Favored : 89.81 % Rotamer: Outliers : 0.16 % Allowed : 3.78 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % 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: -3.03 (0.12), residues: 4377 helix: -1.05 (0.18), residues: 679 sheet: -1.64 (0.21), residues: 587 loop : -2.49 (0.10), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 995 TYR 0.030 0.002 TYR A 873 PHE 0.035 0.002 PHE E1089 TRP 0.026 0.001 TRP L 41 HIS 0.008 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00290 (36349) covalent geometry : angle 0.72443 (49459) SS BOND : bond 0.00399 ( 48) SS BOND : angle 1.42110 ( 96) hydrogen bonds : bond 0.04948 ( 735) hydrogen bonds : angle 7.05157 ( 1944) Misc. bond : bond 0.00075 ( 2) link_ALPHA1-3 : bond 0.01605 ( 5) link_ALPHA1-3 : angle 2.20716 ( 15) link_ALPHA1-6 : bond 0.00657 ( 8) link_ALPHA1-6 : angle 1.99388 ( 24) link_BETA1-2 : bond 0.00673 ( 1) link_BETA1-2 : angle 0.26881 ( 3) link_BETA1-4 : bond 0.00837 ( 36) link_BETA1-4 : angle 2.72394 ( 108) link_BETA1-6 : bond 0.00927 ( 5) link_BETA1-6 : angle 1.57960 ( 15) link_NAG-ASN : bond 0.00648 ( 43) link_NAG-ASN : angle 4.02568 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 533 time to evaluate : 1.281 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: A 104 TRP cc_start: 0.4787 (m-10) cc_final: 0.4547 (m-10) REVERT: A 220 PHE cc_start: 0.8082 (p90) cc_final: 0.7746 (p90) REVERT: A 298 GLU cc_start: 0.8631 (tp30) cc_final: 0.8311 (tp30) REVERT: A 953 ASN cc_start: 0.8086 (m110) cc_final: 0.7808 (m110) REVERT: A 1014 ARG cc_start: 0.8410 (tpp-160) cc_final: 0.8169 (tpp80) REVERT: A 1052 PHE cc_start: 0.8929 (m-10) cc_final: 0.8711 (m-10) REVERT: A 1064 HIS cc_start: 0.8165 (m170) cc_final: 0.7851 (m170) REVERT: C 44 ARG cc_start: 0.8673 (ptt-90) cc_final: 0.8026 (ptt180) REVERT: C 80 ASP cc_start: 0.8414 (t0) cc_final: 0.7960 (t0) REVERT: C 224 GLU cc_start: 0.6610 (pp20) cc_final: 0.6288 (pp20) REVERT: C 354 ASN cc_start: 0.9433 (t0) cc_final: 0.9077 (t0) REVERT: C 396 TYR cc_start: 0.8664 (m-80) cc_final: 0.8173 (m-80) REVERT: C 765 ARG cc_start: 0.8699 (tmt-80) cc_final: 0.8438 (ptm-80) REVERT: C 790 LYS cc_start: 0.7870 (mmpt) cc_final: 0.7615 (mmmt) REVERT: C 900 MET cc_start: 0.3924 (mpp) cc_final: 0.3475 (mpp) REVERT: C 996 LEU cc_start: 0.8371 (mm) cc_final: 0.8152 (mm) REVERT: C 1052 PHE cc_start: 0.8518 (m-10) cc_final: 0.7410 (m-10) REVERT: C 1055 SER cc_start: 0.9186 (t) cc_final: 0.8984 (t) REVERT: C 1110 TYR cc_start: 0.8638 (t80) cc_final: 0.8323 (t80) REVERT: C 1114 ILE cc_start: 0.8108 (mm) cc_final: 0.7752 (tp) REVERT: E 53 ASP cc_start: 0.7012 (t70) cc_final: 0.6646 (t70) REVERT: E 104 TRP cc_start: 0.5412 (m100) cc_final: 0.4976 (m100) REVERT: E 106 PHE cc_start: 0.6384 (m-10) cc_final: 0.6122 (m-10) REVERT: E 205 SER cc_start: 0.7216 (p) cc_final: 0.6735 (m) REVERT: E 328 ARG cc_start: 0.7120 (mmm160) cc_final: 0.6890 (mmm160) REVERT: E 737 ASP cc_start: 0.8004 (p0) cc_final: 0.7536 (p0) REVERT: E 775 ASP cc_start: 0.8713 (p0) cc_final: 0.8392 (p0) REVERT: E 784 GLN cc_start: 0.7346 (tm-30) cc_final: 0.7055 (tm-30) REVERT: E 800 PHE cc_start: 0.7145 (m-80) cc_final: 0.6517 (m-80) REVERT: E 925 ASN cc_start: 0.8929 (m110) cc_final: 0.8478 (m-40) REVERT: E 950 ASP cc_start: 0.8271 (m-30) cc_final: 0.7688 (m-30) REVERT: E 962 LEU cc_start: 0.9337 (tp) cc_final: 0.9133 (tp) REVERT: E 1007 TYR cc_start: 0.7960 (t80) cc_final: 0.7251 (t80) REVERT: E 1050 MET cc_start: 0.7561 (ppp) cc_final: 0.7160 (ppp) REVERT: H 47 TRP cc_start: 0.6025 (t60) cc_final: 0.5159 (t60) REVERT: I 98 TYR cc_start: 0.8591 (t80) cc_final: 0.7971 (t80) REVERT: L 4 MET cc_start: 0.4852 (mtp) cc_final: 0.1957 (mpp) REVERT: L 109 LYS cc_start: 0.6756 (tttt) cc_final: 0.6166 (tptt) outliers start: 6 outliers final: 1 residues processed: 537 average time/residue: 0.1924 time to fit residues: 173.3202 Evaluate side-chains 424 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 423 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 358 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 385 optimal weight: 0.9980 chunk 342 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 117 optimal weight: 0.0870 overall best weight: 1.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN A 960 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 856 ASN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN ** E 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E 955 ASN ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.174117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.149385 restraints weight = 145547.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.150724 restraints weight = 109665.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.151880 restraints weight = 88539.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.152450 restraints weight = 75026.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.152482 restraints weight = 66791.442| |-----------------------------------------------------------------------------| r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36497 Z= 0.146 Angle : 0.774 19.935 49849 Z= 0.375 Chirality : 0.051 0.420 5919 Planarity : 0.006 0.125 6211 Dihedral : 9.731 71.160 6735 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.10 % Favored : 89.79 % Rotamer: Outliers : 0.13 % Allowed : 2.34 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % 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: -2.98 (0.12), residues: 4377 helix: -1.02 (0.19), residues: 672 sheet: -1.63 (0.21), residues: 600 loop : -2.45 (0.10), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 995 TYR 0.038 0.002 TYR C 873 PHE 0.040 0.002 PHE H 29 TRP 0.018 0.001 TRP C 436 HIS 0.008 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00311 (36349) covalent geometry : angle 0.73062 (49459) SS BOND : bond 0.00361 ( 48) SS BOND : angle 1.25302 ( 96) hydrogen bonds : bond 0.04899 ( 735) hydrogen bonds : angle 6.99129 ( 1944) Misc. bond : bond 0.00067 ( 2) link_ALPHA1-3 : bond 0.01538 ( 5) link_ALPHA1-3 : angle 2.35217 ( 15) link_ALPHA1-6 : bond 0.00613 ( 8) link_ALPHA1-6 : angle 1.89622 ( 24) link_BETA1-2 : bond 0.00656 ( 1) link_BETA1-2 : angle 0.39933 ( 3) link_BETA1-4 : bond 0.00842 ( 36) link_BETA1-4 : angle 2.68800 ( 108) link_BETA1-6 : bond 0.00811 ( 5) link_BETA1-6 : angle 1.45622 ( 15) link_NAG-ASN : bond 0.00689 ( 43) link_NAG-ASN : angle 4.28066 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 524 time to evaluate : 1.126 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: A 92 PHE cc_start: 0.6722 (t80) cc_final: 0.6477 (t80) REVERT: A 220 PHE cc_start: 0.8090 (p90) cc_final: 0.7771 (p90) REVERT: A 298 GLU cc_start: 0.8617 (tp30) cc_final: 0.8316 (tp30) REVERT: A 314 GLN cc_start: 0.7615 (tm-30) cc_final: 0.7257 (tm-30) REVERT: A 779 GLN cc_start: 0.8851 (tp-100) cc_final: 0.8650 (tp-100) REVERT: A 953 ASN cc_start: 0.8136 (m110) cc_final: 0.7860 (m110) REVERT: A 1010 GLN cc_start: 0.8866 (tp-100) cc_final: 0.8603 (tp-100) REVERT: A 1014 ARG cc_start: 0.8744 (tpp-160) cc_final: 0.8227 (tpp80) REVERT: A 1019 ARG cc_start: 0.8490 (ptp-170) cc_final: 0.8055 (ptt-90) REVERT: A 1028 LYS cc_start: 0.9429 (mttm) cc_final: 0.9202 (mttt) REVERT: A 1064 HIS cc_start: 0.8133 (m170) cc_final: 0.7715 (m170) REVERT: C 44 ARG cc_start: 0.8691 (ptt-90) cc_final: 0.8139 (ptt180) REVERT: C 80 ASP cc_start: 0.8401 (t0) cc_final: 0.7982 (t0) REVERT: C 224 GLU cc_start: 0.6600 (pp20) cc_final: 0.6305 (pp20) REVERT: C 354 ASN cc_start: 0.9444 (t0) cc_final: 0.9175 (t0) REVERT: C 396 TYR cc_start: 0.8590 (m-80) cc_final: 0.8314 (m-80) REVERT: C 770 ILE cc_start: 0.9455 (mt) cc_final: 0.9150 (mt) REVERT: C 790 LYS cc_start: 0.7762 (mmpt) cc_final: 0.7549 (mmmt) REVERT: C 902 MET cc_start: 0.8264 (pmm) cc_final: 0.7367 (pmm) REVERT: C 1018 ILE cc_start: 0.9313 (mt) cc_final: 0.8895 (mt) REVERT: C 1052 PHE cc_start: 0.8310 (m-10) cc_final: 0.7049 (m-10) REVERT: C 1103 PHE cc_start: 0.8071 (m-80) cc_final: 0.7802 (m-80) REVERT: C 1110 TYR cc_start: 0.8596 (t80) cc_final: 0.8300 (t80) REVERT: C 1114 ILE cc_start: 0.8097 (mm) cc_final: 0.7730 (tp) REVERT: E 53 ASP cc_start: 0.7162 (t70) cc_final: 0.6788 (t70) REVERT: E 104 TRP cc_start: 0.5441 (m100) cc_final: 0.5183 (m100) REVERT: E 106 PHE cc_start: 0.6342 (m-10) cc_final: 0.6060 (m-10) REVERT: E 205 SER cc_start: 0.7273 (p) cc_final: 0.6816 (m) REVERT: E 737 ASP cc_start: 0.8059 (p0) cc_final: 0.7612 (p0) REVERT: E 775 ASP cc_start: 0.8795 (p0) cc_final: 0.8539 (p0) REVERT: E 800 PHE cc_start: 0.7152 (m-80) cc_final: 0.6654 (m-80) REVERT: E 950 ASP cc_start: 0.8296 (m-30) cc_final: 0.7767 (m-30) REVERT: E 962 LEU cc_start: 0.9332 (tp) cc_final: 0.9127 (tp) REVERT: E 1007 TYR cc_start: 0.8198 (t80) cc_final: 0.7491 (t80) REVERT: E 1010 GLN cc_start: 0.8583 (tp40) cc_final: 0.8242 (tp40) REVERT: E 1111 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8305 (tm-30) REVERT: H 47 TRP cc_start: 0.5869 (t60) cc_final: 0.4668 (t60) REVERT: I 98 TYR cc_start: 0.8419 (t80) cc_final: 0.7759 (t80) REVERT: L 4 MET cc_start: 0.4646 (mtp) cc_final: 0.1876 (mpp) REVERT: L 109 LYS cc_start: 0.6928 (tttt) cc_final: 0.6304 (tptt) outliers start: 5 outliers final: 0 residues processed: 528 average time/residue: 0.1899 time to fit residues: 167.9422 Evaluate side-chains 418 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 336 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 286 optimal weight: 0.7980 chunk 167 optimal weight: 9.9990 chunk 332 optimal weight: 8.9990 chunk 147 optimal weight: 3.9990 chunk 218 optimal weight: 0.0870 chunk 271 optimal weight: 0.6980 chunk 377 optimal weight: 5.9990 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 969 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 762 GLN C 856 ASN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN ** E 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E 955 ASN ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1023 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.170533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.135757 restraints weight = 125542.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.139107 restraints weight = 81548.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.141363 restraints weight = 58480.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.143164 restraints weight = 45881.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.143963 restraints weight = 38092.869| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 36497 Z= 0.148 Angle : 0.772 19.981 49849 Z= 0.376 Chirality : 0.050 0.421 5919 Planarity : 0.005 0.097 6211 Dihedral : 9.271 69.581 6735 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.30 % Favored : 89.60 % Rotamer: Outliers : 0.13 % Allowed : 2.24 % Favored : 97.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.95 (0.12), residues: 4377 helix: -1.00 (0.18), residues: 676 sheet: -1.63 (0.21), residues: 579 loop : -2.43 (0.10), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 995 TYR 0.031 0.002 TYR A 873 PHE 0.027 0.002 PHE H 29 TRP 0.035 0.002 TRP L 41 HIS 0.025 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00316 (36349) covalent geometry : angle 0.72897 (49459) SS BOND : bond 0.00341 ( 48) SS BOND : angle 1.19165 ( 96) hydrogen bonds : bond 0.04932 ( 735) hydrogen bonds : angle 6.99367 ( 1944) Misc. bond : bond 0.00091 ( 2) link_ALPHA1-3 : bond 0.01593 ( 5) link_ALPHA1-3 : angle 2.35873 ( 15) link_ALPHA1-6 : bond 0.00619 ( 8) link_ALPHA1-6 : angle 1.85440 ( 24) link_BETA1-2 : bond 0.00663 ( 1) link_BETA1-2 : angle 0.44861 ( 3) link_BETA1-4 : bond 0.00800 ( 36) link_BETA1-4 : angle 2.58499 ( 108) link_BETA1-6 : bond 0.00767 ( 5) link_BETA1-6 : angle 1.33834 ( 15) link_NAG-ASN : bond 0.00647 ( 43) link_NAG-ASN : angle 4.31160 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 527 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: A 92 PHE cc_start: 0.6850 (t80) cc_final: 0.6543 (t80) REVERT: A 220 PHE cc_start: 0.8037 (p90) cc_final: 0.7761 (p90) REVERT: A 298 GLU cc_start: 0.8633 (tp30) cc_final: 0.8327 (tp30) REVERT: A 314 GLN cc_start: 0.7715 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 773 GLU cc_start: 0.7628 (tm-30) cc_final: 0.6772 (tm-30) REVERT: A 777 ASN cc_start: 0.8747 (m110) cc_final: 0.8251 (m110) REVERT: A 779 GLN cc_start: 0.8818 (tp-100) cc_final: 0.8603 (tp-100) REVERT: A 905 ARG cc_start: 0.6985 (ptp-110) cc_final: 0.6733 (ptp-170) REVERT: A 953 ASN cc_start: 0.8429 (m110) cc_final: 0.8218 (m110) REVERT: A 957 GLN cc_start: 0.9038 (mp10) cc_final: 0.8738 (pm20) REVERT: A 1014 ARG cc_start: 0.8316 (tpp-160) cc_final: 0.7840 (tpp80) REVERT: A 1028 LYS cc_start: 0.9511 (mttm) cc_final: 0.9238 (mttt) REVERT: A 1052 PHE cc_start: 0.9028 (m-10) cc_final: 0.8350 (m-10) REVERT: A 1064 HIS cc_start: 0.8344 (m170) cc_final: 0.7891 (m170) REVERT: C 44 ARG cc_start: 0.8679 (ptt-90) cc_final: 0.8081 (ptt180) REVERT: C 80 ASP cc_start: 0.8417 (t0) cc_final: 0.8012 (t0) REVERT: C 312 ILE cc_start: 0.9063 (pt) cc_final: 0.8778 (pt) REVERT: C 354 ASN cc_start: 0.9449 (t0) cc_final: 0.9187 (t0) REVERT: C 396 TYR cc_start: 0.8559 (m-80) cc_final: 0.8275 (m-80) REVERT: C 742 ILE cc_start: 0.8876 (mm) cc_final: 0.8368 (mm) REVERT: C 777 ASN cc_start: 0.8908 (m110) cc_final: 0.8699 (m110) REVERT: C 790 LYS cc_start: 0.7916 (mmpt) cc_final: 0.7544 (mmmt) REVERT: C 817 PHE cc_start: 0.8160 (t80) cc_final: 0.7957 (t80) REVERT: C 873 TYR cc_start: 0.8080 (m-10) cc_final: 0.7872 (m-80) REVERT: C 900 MET cc_start: 0.3756 (mpp) cc_final: 0.3287 (mpp) REVERT: C 902 MET cc_start: 0.8328 (pmm) cc_final: 0.7573 (pmm) REVERT: C 1004 LEU cc_start: 0.9311 (mt) cc_final: 0.8977 (mt) REVERT: C 1018 ILE cc_start: 0.9261 (mt) cc_final: 0.8738 (mt) REVERT: C 1052 PHE cc_start: 0.8050 (m-10) cc_final: 0.7122 (m-10) REVERT: C 1103 PHE cc_start: 0.8102 (m-80) cc_final: 0.7457 (m-80) REVERT: C 1110 TYR cc_start: 0.8616 (t80) cc_final: 0.8211 (t80) REVERT: C 1114 ILE cc_start: 0.7893 (mm) cc_final: 0.7512 (tp) REVERT: E 53 ASP cc_start: 0.7143 (t70) cc_final: 0.6733 (t70) REVERT: E 104 TRP cc_start: 0.5322 (m100) cc_final: 0.5047 (m100) REVERT: E 106 PHE cc_start: 0.6490 (m-10) cc_final: 0.6246 (m-10) REVERT: E 205 SER cc_start: 0.7340 (p) cc_final: 0.6892 (m) REVERT: E 737 ASP cc_start: 0.8074 (p0) cc_final: 0.7656 (p0) REVERT: E 775 ASP cc_start: 0.8716 (p0) cc_final: 0.8368 (p0) REVERT: E 800 PHE cc_start: 0.7170 (m-80) cc_final: 0.6624 (m-80) REVERT: E 918 GLU cc_start: 0.8999 (tt0) cc_final: 0.8630 (tm-30) REVERT: E 925 ASN cc_start: 0.9011 (m110) cc_final: 0.8580 (m-40) REVERT: E 926 GLN cc_start: 0.9269 (pm20) cc_final: 0.8901 (pm20) REVERT: E 950 ASP cc_start: 0.8316 (m-30) cc_final: 0.7757 (m-30) REVERT: E 962 LEU cc_start: 0.9334 (tp) cc_final: 0.9105 (tp) REVERT: E 1007 TYR cc_start: 0.7927 (t80) cc_final: 0.7174 (t80) REVERT: E 1010 GLN cc_start: 0.8199 (tp40) cc_final: 0.7826 (tp-100) REVERT: E 1050 MET cc_start: 0.7510 (ppp) cc_final: 0.7188 (ppp) REVERT: E 1111 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8363 (tm-30) REVERT: H 47 TRP cc_start: 0.5866 (t60) cc_final: 0.4957 (t60) REVERT: I 98 TYR cc_start: 0.8509 (t80) cc_final: 0.8022 (t80) REVERT: L 4 MET cc_start: 0.4993 (mtp) cc_final: 0.2211 (mpp) REVERT: L 109 LYS cc_start: 0.6805 (tttt) cc_final: 0.6241 (tptt) outliers start: 5 outliers final: 0 residues processed: 531 average time/residue: 0.1891 time to fit residues: 167.9426 Evaluate side-chains 427 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 111 optimal weight: 10.0000 chunk 421 optimal weight: 2.9990 chunk 309 optimal weight: 0.5980 chunk 425 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 chunk 220 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 96 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 361 optimal weight: 30.0000 chunk 75 optimal weight: 3.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 960 ASN A 969 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 856 ASN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN ** E 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E 955 ASN ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN L 95 GLN L 205 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.167097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.132647 restraints weight = 125044.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.135763 restraints weight = 83348.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.137769 restraints weight = 60193.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.139501 restraints weight = 48220.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.140391 restraints weight = 40443.046| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 36497 Z= 0.205 Angle : 0.834 20.120 49849 Z= 0.408 Chirality : 0.052 0.490 5919 Planarity : 0.006 0.101 6211 Dihedral : 9.381 69.545 6735 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.22 % Favored : 87.66 % Rotamer: Outliers : 0.10 % Allowed : 1.75 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.05 (0.12), residues: 4377 helix: -1.11 (0.18), residues: 677 sheet: -1.79 (0.21), residues: 562 loop : -2.46 (0.10), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 995 TYR 0.031 0.002 TYR C 313 PHE 0.043 0.002 PHE C 55 TRP 0.032 0.002 TRP C 152 HIS 0.017 0.002 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00432 (36349) covalent geometry : angle 0.78556 (49459) SS BOND : bond 0.00444 ( 48) SS BOND : angle 1.26346 ( 96) hydrogen bonds : bond 0.05511 ( 735) hydrogen bonds : angle 7.18528 ( 1944) Misc. bond : bond 0.00093 ( 2) link_ALPHA1-3 : bond 0.01541 ( 5) link_ALPHA1-3 : angle 2.55387 ( 15) link_ALPHA1-6 : bond 0.00605 ( 8) link_ALPHA1-6 : angle 1.80208 ( 24) link_BETA1-2 : bond 0.00612 ( 1) link_BETA1-2 : angle 0.49493 ( 3) link_BETA1-4 : bond 0.00763 ( 36) link_BETA1-4 : angle 2.55419 ( 108) link_BETA1-6 : bond 0.00711 ( 5) link_BETA1-6 : angle 1.42511 ( 15) link_NAG-ASN : bond 0.00749 ( 43) link_NAG-ASN : angle 4.90063 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 533 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8053 (p90) cc_final: 0.7760 (p90) REVERT: A 298 GLU cc_start: 0.8670 (tp30) cc_final: 0.8367 (tp30) REVERT: A 314 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7473 (tm-30) REVERT: A 723 THR cc_start: 0.8923 (p) cc_final: 0.8391 (p) REVERT: A 779 GLN cc_start: 0.8839 (tp-100) cc_final: 0.8526 (tp-100) REVERT: A 877 LEU cc_start: 0.9167 (mt) cc_final: 0.8927 (mt) REVERT: A 882 ILE cc_start: 0.9483 (mt) cc_final: 0.9270 (mt) REVERT: A 957 GLN cc_start: 0.8881 (mp10) cc_final: 0.8538 (mp10) REVERT: A 1014 ARG cc_start: 0.8410 (tpp-160) cc_final: 0.8149 (tpp80) REVERT: A 1028 LYS cc_start: 0.9510 (mttm) cc_final: 0.9176 (mttt) REVERT: A 1052 PHE cc_start: 0.9027 (m-10) cc_final: 0.8504 (m-10) REVERT: A 1064 HIS cc_start: 0.8412 (m170) cc_final: 0.7742 (m170) REVERT: C 80 ASP cc_start: 0.8405 (t0) cc_final: 0.7936 (t0) REVERT: C 312 ILE cc_start: 0.8991 (pt) cc_final: 0.8788 (pt) REVERT: C 354 ASN cc_start: 0.9505 (t0) cc_final: 0.9262 (t0) REVERT: C 396 TYR cc_start: 0.8553 (m-80) cc_final: 0.8264 (m-80) REVERT: C 742 ILE cc_start: 0.8836 (mm) cc_final: 0.8474 (mm) REVERT: C 790 LYS cc_start: 0.7960 (mmpt) cc_final: 0.7507 (mmmt) REVERT: C 817 PHE cc_start: 0.8113 (t80) cc_final: 0.7894 (t80) REVERT: C 900 MET cc_start: 0.3983 (mpp) cc_final: 0.3346 (mpp) REVERT: C 902 MET cc_start: 0.8305 (pmm) cc_final: 0.7407 (pmm) REVERT: C 965 GLN cc_start: 0.9526 (mp10) cc_final: 0.9193 (mp10) REVERT: C 1018 ILE cc_start: 0.9277 (mt) cc_final: 0.8765 (mt) REVERT: C 1052 PHE cc_start: 0.8451 (m-10) cc_final: 0.7185 (m-10) REVERT: C 1114 ILE cc_start: 0.7910 (mm) cc_final: 0.7519 (tp) REVERT: E 53 ASP cc_start: 0.7276 (t70) cc_final: 0.6769 (t70) REVERT: E 106 PHE cc_start: 0.6644 (m-10) cc_final: 0.6382 (m-10) REVERT: E 205 SER cc_start: 0.7283 (p) cc_final: 0.6819 (m) REVERT: E 737 ASP cc_start: 0.8031 (p0) cc_final: 0.7592 (p0) REVERT: E 780 GLU cc_start: 0.7261 (tp30) cc_final: 0.7032 (tp30) REVERT: E 800 PHE cc_start: 0.7180 (m-80) cc_final: 0.6698 (m-80) REVERT: E 918 GLU cc_start: 0.8911 (tt0) cc_final: 0.8531 (tm-30) REVERT: E 950 ASP cc_start: 0.8337 (m-30) cc_final: 0.7866 (m-30) REVERT: E 1007 TYR cc_start: 0.8018 (t80) cc_final: 0.7217 (t80) REVERT: E 1010 GLN cc_start: 0.8151 (tp40) cc_final: 0.7815 (tp-100) REVERT: E 1050 MET cc_start: 0.7739 (ppp) cc_final: 0.7440 (ppp) REVERT: E 1111 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8285 (tm-30) REVERT: H 47 TRP cc_start: 0.6025 (t60) cc_final: 0.5107 (t60) REVERT: I 60 ARG cc_start: 0.4603 (ptt-90) cc_final: 0.3282 (pmt170) REVERT: I 98 TYR cc_start: 0.8547 (t80) cc_final: 0.8106 (t80) REVERT: K 81 MET cc_start: 0.4109 (tpt) cc_final: 0.3618 (tpt) REVERT: L 4 MET cc_start: 0.4933 (mtp) cc_final: 0.2243 (mpp) REVERT: L 109 LYS cc_start: 0.6758 (tttt) cc_final: 0.6310 (tptt) outliers start: 4 outliers final: 0 residues processed: 537 average time/residue: 0.1951 time to fit residues: 174.8914 Evaluate side-chains 414 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 313 optimal weight: 1.9990 chunk 306 optimal weight: 6.9990 chunk 207 optimal weight: 10.0000 chunk 327 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 233 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 36 optimal weight: 30.0000 chunk 181 optimal weight: 2.9990 chunk 375 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E 955 ASN ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN K 6 GLN L 95 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.166450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.132397 restraints weight = 123561.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.135963 restraints weight = 83612.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.136998 restraints weight = 63875.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.138795 restraints weight = 49852.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.139680 restraints weight = 41139.157| |-----------------------------------------------------------------------------| r_work (final): 0.4083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 36497 Z= 0.204 Angle : 0.848 20.105 49849 Z= 0.418 Chirality : 0.053 0.559 5919 Planarity : 0.006 0.105 6211 Dihedral : 9.326 70.497 6735 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.90 % Favored : 87.98 % Rotamer: Outliers : 0.08 % Allowed : 0.86 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.12 (0.12), residues: 4377 helix: -1.22 (0.18), residues: 673 sheet: -1.84 (0.21), residues: 551 loop : -2.49 (0.10), residues: 3153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 995 TYR 0.044 0.002 TYR E 707 PHE 0.028 0.002 PHE C 55 TRP 0.048 0.002 TRP F 41 HIS 0.015 0.002 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00434 (36349) covalent geometry : angle 0.80465 (49459) SS BOND : bond 0.00463 ( 48) SS BOND : angle 1.43344 ( 96) hydrogen bonds : bond 0.05570 ( 735) hydrogen bonds : angle 7.34484 ( 1944) Misc. bond : bond 0.00097 ( 2) link_ALPHA1-3 : bond 0.01586 ( 5) link_ALPHA1-3 : angle 2.54634 ( 15) link_ALPHA1-6 : bond 0.00608 ( 8) link_ALPHA1-6 : angle 1.78977 ( 24) link_BETA1-2 : bond 0.00610 ( 1) link_BETA1-2 : angle 0.60763 ( 3) link_BETA1-4 : bond 0.00764 ( 36) link_BETA1-4 : angle 2.54204 ( 108) link_BETA1-6 : bond 0.00738 ( 5) link_BETA1-6 : angle 1.38360 ( 15) link_NAG-ASN : bond 0.00677 ( 43) link_NAG-ASN : angle 4.56344 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 537 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 PHE cc_start: 0.8030 (p90) cc_final: 0.7780 (p90) REVERT: A 298 GLU cc_start: 0.8666 (tp30) cc_final: 0.8377 (tp30) REVERT: A 314 GLN cc_start: 0.7813 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 723 THR cc_start: 0.9051 (p) cc_final: 0.8529 (p) REVERT: A 773 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7169 (tm-30) REVERT: A 774 GLN cc_start: 0.8451 (mp10) cc_final: 0.8066 (mp-120) REVERT: A 779 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8474 (tp-100) REVERT: A 877 LEU cc_start: 0.9165 (mt) cc_final: 0.8936 (mt) REVERT: A 882 ILE cc_start: 0.9504 (mt) cc_final: 0.9294 (mt) REVERT: A 957 GLN cc_start: 0.8961 (mp10) cc_final: 0.8715 (mp10) REVERT: A 1014 ARG cc_start: 0.8416 (tpp-160) cc_final: 0.8197 (tpp80) REVERT: A 1019 ARG cc_start: 0.8426 (tmt-80) cc_final: 0.8048 (tpp-160) REVERT: A 1028 LYS cc_start: 0.9527 (mttm) cc_final: 0.9313 (mttt) REVERT: A 1052 PHE cc_start: 0.9094 (m-10) cc_final: 0.8506 (m-10) REVERT: A 1064 HIS cc_start: 0.8491 (m170) cc_final: 0.8083 (m-70) REVERT: C 80 ASP cc_start: 0.8482 (t0) cc_final: 0.7956 (t0) REVERT: C 224 GLU cc_start: 0.6736 (pp20) cc_final: 0.6480 (pp20) REVERT: C 312 ILE cc_start: 0.9004 (pt) cc_final: 0.8781 (pt) REVERT: C 354 ASN cc_start: 0.9494 (t0) cc_final: 0.9247 (t0) REVERT: C 396 TYR cc_start: 0.8614 (m-80) cc_final: 0.8311 (m-80) REVERT: C 742 ILE cc_start: 0.8835 (mm) cc_final: 0.8248 (mm) REVERT: C 758 SER cc_start: 0.9389 (t) cc_final: 0.9187 (p) REVERT: C 790 LYS cc_start: 0.8006 (mmpt) cc_final: 0.7526 (mmmt) REVERT: C 900 MET cc_start: 0.3970 (mpp) cc_final: 0.3197 (mpp) REVERT: C 902 MET cc_start: 0.8302 (pmm) cc_final: 0.7334 (pmm) REVERT: C 965 GLN cc_start: 0.9565 (mp10) cc_final: 0.9227 (mp10) REVERT: C 1004 LEU cc_start: 0.9382 (mt) cc_final: 0.9140 (mt) REVERT: C 1018 ILE cc_start: 0.9336 (mt) cc_final: 0.8847 (mt) REVERT: C 1050 MET cc_start: 0.7275 (ttt) cc_final: 0.6936 (ttp) REVERT: C 1052 PHE cc_start: 0.8401 (m-10) cc_final: 0.6704 (m-10) REVERT: E 53 ASP cc_start: 0.7300 (t70) cc_final: 0.6817 (t70) REVERT: E 205 SER cc_start: 0.7280 (p) cc_final: 0.6808 (m) REVERT: E 305 SER cc_start: 0.8221 (m) cc_final: 0.7763 (t) REVERT: E 737 ASP cc_start: 0.8056 (p0) cc_final: 0.7589 (p0) REVERT: E 780 GLU cc_start: 0.7331 (tp30) cc_final: 0.7110 (tp30) REVERT: E 800 PHE cc_start: 0.7248 (m-80) cc_final: 0.6732 (m-80) REVERT: E 918 GLU cc_start: 0.8921 (tt0) cc_final: 0.8475 (tm-30) REVERT: E 950 ASP cc_start: 0.8360 (m-30) cc_final: 0.7846 (m-30) REVERT: E 1007 TYR cc_start: 0.8162 (t80) cc_final: 0.7280 (t80) REVERT: E 1010 GLN cc_start: 0.8313 (tp40) cc_final: 0.7964 (tp-100) REVERT: E 1111 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8365 (tm-30) REVERT: H 47 TRP cc_start: 0.6119 (t60) cc_final: 0.4899 (t60) REVERT: I 60 ARG cc_start: 0.4685 (ptt-90) cc_final: 0.3377 (pmt170) REVERT: I 98 TYR cc_start: 0.8572 (t80) cc_final: 0.8076 (t80) REVERT: K 11 MET cc_start: 0.6106 (tmm) cc_final: 0.5764 (tmm) REVERT: K 81 MET cc_start: 0.3913 (tpt) cc_final: 0.3475 (tpt) REVERT: L 4 MET cc_start: 0.5020 (mtp) cc_final: 0.2134 (mpp) REVERT: L 109 LYS cc_start: 0.6886 (tttt) cc_final: 0.6424 (tptt) outliers start: 3 outliers final: 0 residues processed: 540 average time/residue: 0.1910 time to fit residues: 173.8429 Evaluate side-chains 411 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 387 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 397 optimal weight: 7.9990 chunk 165 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 317 optimal weight: 9.9990 chunk 281 optimal weight: 6.9990 chunk 247 optimal weight: 0.7980 chunk 261 optimal weight: 0.9980 chunk 395 optimal weight: 1.9990 chunk 306 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A 969 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 901 GLN ** E 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E 955 ASN ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.169837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.137271 restraints weight = 126436.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.139999 restraints weight = 86381.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.142105 restraints weight = 64711.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.143499 restraints weight = 47645.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.143986 restraints weight = 41091.958| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 36497 Z= 0.154 Angle : 0.808 20.028 49849 Z= 0.396 Chirality : 0.052 0.569 5919 Planarity : 0.006 0.106 6211 Dihedral : 8.987 69.008 6735 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.78 % Favored : 89.12 % Rotamer: Outliers : 0.08 % Allowed : 0.47 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.21 % 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: -3.04 (0.12), residues: 4377 helix: -1.09 (0.19), residues: 683 sheet: -1.81 (0.21), residues: 576 loop : -2.46 (0.10), residues: 3118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 995 TYR 0.045 0.002 TYR C1007 PHE 0.032 0.002 PHE C 55 TRP 0.029 0.002 TRP L 41 HIS 0.014 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00335 (36349) covalent geometry : angle 0.76612 (49459) SS BOND : bond 0.00425 ( 48) SS BOND : angle 1.41992 ( 96) hydrogen bonds : bond 0.05088 ( 735) hydrogen bonds : angle 7.12595 ( 1944) Misc. bond : bond 0.00077 ( 2) link_ALPHA1-3 : bond 0.01545 ( 5) link_ALPHA1-3 : angle 2.47191 ( 15) link_ALPHA1-6 : bond 0.00618 ( 8) link_ALPHA1-6 : angle 1.78344 ( 24) link_BETA1-2 : bond 0.00643 ( 1) link_BETA1-2 : angle 0.51678 ( 3) link_BETA1-4 : bond 0.00775 ( 36) link_BETA1-4 : angle 2.47415 ( 108) link_BETA1-6 : bond 0.00727 ( 5) link_BETA1-6 : angle 1.23815 ( 15) link_NAG-ASN : bond 0.00640 ( 43) link_NAG-ASN : angle 4.38799 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8754 Ramachandran restraints generated. 4377 Oldfield, 0 Emsley, 4377 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 521 time to evaluate : 1.264 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: A 92 PHE cc_start: 0.6828 (t80) cc_final: 0.6548 (t80) REVERT: A 220 PHE cc_start: 0.8035 (p90) cc_final: 0.7776 (p90) REVERT: A 298 GLU cc_start: 0.8609 (tp30) cc_final: 0.8307 (tp30) REVERT: A 314 GLN cc_start: 0.7750 (tm-30) cc_final: 0.7360 (tm-30) REVERT: A 723 THR cc_start: 0.8897 (p) cc_final: 0.8580 (p) REVERT: A 765 ARG cc_start: 0.8837 (pmt-80) cc_final: 0.8613 (pmt-80) REVERT: A 770 ILE cc_start: 0.9281 (mt) cc_final: 0.9064 (mt) REVERT: A 773 GLU cc_start: 0.7789 (tm-30) cc_final: 0.6829 (tm-30) REVERT: A 774 GLN cc_start: 0.8292 (mp10) cc_final: 0.7994 (mp10) REVERT: A 779 GLN cc_start: 0.8735 (tp-100) cc_final: 0.8386 (tp-100) REVERT: A 882 ILE cc_start: 0.9312 (mt) cc_final: 0.9083 (mt) REVERT: A 957 GLN cc_start: 0.8868 (mp10) cc_final: 0.8574 (mp10) REVERT: A 1019 ARG cc_start: 0.8106 (tmt-80) cc_final: 0.7798 (tpp-160) REVERT: A 1052 PHE cc_start: 0.8907 (m-10) cc_final: 0.8250 (m-10) REVERT: A 1064 HIS cc_start: 0.8344 (m170) cc_final: 0.7854 (m170) REVERT: C 80 ASP cc_start: 0.8452 (t0) cc_final: 0.7925 (t0) REVERT: C 224 GLU cc_start: 0.6708 (pp20) cc_final: 0.6418 (pp20) REVERT: C 354 ASN cc_start: 0.9489 (t0) cc_final: 0.9260 (t0) REVERT: C 396 TYR cc_start: 0.8528 (m-80) cc_final: 0.8021 (m-80) REVERT: C 742 ILE cc_start: 0.8820 (mm) cc_final: 0.8584 (mm) REVERT: C 777 ASN cc_start: 0.8820 (m110) cc_final: 0.8541 (m110) REVERT: C 790 LYS cc_start: 0.7975 (mmpt) cc_final: 0.7563 (mmmt) REVERT: C 900 MET cc_start: 0.3848 (mpp) cc_final: 0.3079 (mpp) REVERT: C 902 MET cc_start: 0.8346 (pmm) cc_final: 0.7316 (pmm) REVERT: C 926 GLN cc_start: 0.8657 (pm20) cc_final: 0.8379 (pm20) REVERT: C 957 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8396 (tm-30) REVERT: C 1018 ILE cc_start: 0.9215 (mt) cc_final: 0.8826 (mt) REVERT: C 1052 PHE cc_start: 0.8408 (m-10) cc_final: 0.6674 (m-10) REVERT: C 1063 LEU cc_start: 0.9074 (mp) cc_final: 0.8835 (mt) REVERT: E 53 ASP cc_start: 0.7048 (t70) cc_final: 0.6540 (t70) REVERT: E 106 PHE cc_start: 0.6143 (m-10) cc_final: 0.5856 (m-10) REVERT: E 205 SER cc_start: 0.7200 (p) cc_final: 0.6691 (m) REVERT: E 305 SER cc_start: 0.8260 (m) cc_final: 0.7764 (t) REVERT: E 645 THR cc_start: 0.9051 (p) cc_final: 0.8552 (t) REVERT: E 675 GLN cc_start: 0.8817 (tp-100) cc_final: 0.8082 (tp40) REVERT: E 737 ASP cc_start: 0.8001 (p0) cc_final: 0.7589 (p0) REVERT: E 800 PHE cc_start: 0.7118 (m-80) cc_final: 0.6918 (m-80) REVERT: E 873 TYR cc_start: 0.8399 (m-80) cc_final: 0.8164 (m-80) REVERT: E 918 GLU cc_start: 0.8904 (tt0) cc_final: 0.8401 (tm-30) REVERT: E 950 ASP cc_start: 0.8277 (m-30) cc_final: 0.7744 (m-30) REVERT: E 1007 TYR cc_start: 0.7908 (t80) cc_final: 0.7093 (t80) REVERT: E 1010 GLN cc_start: 0.8137 (tp40) cc_final: 0.7795 (tp-100) REVERT: E 1111 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8381 (tm-30) REVERT: I 98 TYR cc_start: 0.8517 (t80) cc_final: 0.8022 (t80) REVERT: K 11 MET cc_start: 0.6267 (tmm) cc_final: 0.5933 (tmm) REVERT: L 4 MET cc_start: 0.4464 (mtp) cc_final: 0.2079 (mpp) REVERT: L 109 LYS cc_start: 0.6786 (tttt) cc_final: 0.6369 (tptt) outliers start: 3 outliers final: 0 residues processed: 524 average time/residue: 0.1938 time to fit residues: 170.4922 Evaluate side-chains 419 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 436 random chunks: chunk 268 optimal weight: 1.9990 chunk 279 optimal weight: 1.9990 chunk 314 optimal weight: 0.0020 chunk 113 optimal weight: 8.9990 chunk 241 optimal weight: 9.9990 chunk 329 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 384 optimal weight: 0.4980 chunk 112 optimal weight: 7.9990 chunk 368 optimal weight: 20.0000 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1054 GLN ** A1064 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 787 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 920 GLN E 928 ASN E 955 ASN ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.171351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.137031 restraints weight = 121919.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.139942 restraints weight = 80150.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.142018 restraints weight = 58056.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.143289 restraints weight = 45966.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.144724 restraints weight = 39128.316| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 36497 Z= 0.144 Angle : 0.817 22.615 49849 Z= 0.397 Chirality : 0.052 0.535 5919 Planarity : 0.006 0.104 6211 Dihedral : 8.698 66.364 6735 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.05 % Favored : 89.86 % Rotamer: Outliers : 0.08 % Allowed : 0.39 % Favored : 99.53 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 7.21 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.12), residues: 4377 helix: -1.13 (0.19), residues: 678 sheet: -1.75 (0.21), residues: 593 loop : -2.39 (0.11), residues: 3106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 995 TYR 0.036 0.002 TYR A 873 PHE 0.031 0.002 PHE C 55 TRP 0.018 0.002 TRP A1102 HIS 0.013 0.001 HIS E1064 Details of bonding type rmsd covalent geometry : bond 0.00312 (36349) covalent geometry : angle 0.76535 (49459) SS BOND : bond 0.00338 ( 48) SS BOND : angle 1.40628 ( 96) hydrogen bonds : bond 0.04795 ( 735) hydrogen bonds : angle 7.00214 ( 1944) Misc. bond : bond 0.00066 ( 2) link_ALPHA1-3 : bond 0.01570 ( 5) link_ALPHA1-3 : angle 2.49726 ( 15) link_ALPHA1-6 : bond 0.00617 ( 8) link_ALPHA1-6 : angle 1.77171 ( 24) link_BETA1-2 : bond 0.00773 ( 1) link_BETA1-2 : angle 0.49713 ( 3) link_BETA1-4 : bond 0.00818 ( 36) link_BETA1-4 : angle 2.50378 ( 108) link_BETA1-6 : bond 0.00700 ( 5) link_BETA1-6 : angle 1.17863 ( 15) link_NAG-ASN : bond 0.00688 ( 43) link_NAG-ASN : angle 5.03023 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6540.09 seconds wall clock time: 114 minutes 19.57 seconds (6859.57 seconds total)