Starting phenix.real_space_refine on Mon Jul 6 13:39:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wuh_32832/07_2026/7wuh_32832.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wuh_32832/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wuh_32832/07_2026/7wuh_32832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wuh_32832/07_2026/7wuh_32832.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wuh_32832/07_2026/7wuh_32832.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wuh_32832/07_2026/7wuh_32832.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wuh_32832/07_2026/7wuh_32832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wuh_32832/07_2026/7wuh_32832.cif" } 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-6108/lib/python3.11/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 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 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 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 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 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 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 chiralities: 2 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 8.34, per 1000 atoms: 0.23 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: 3.79 Conformation dependent library (CDL) restraints added in 1.6 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: 1.29 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: 8.02 Time building geometry restraints manager: 4.85 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 - 18.08: 19069 18.08 - 36.16: 1531 36.16 - 54.24: 239 54.24 - 72.32: 47 72.32 - 90.39: 29 Dihedral angle restraints: 20915 sinusoidal: 8017 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 20912 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: 6.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.910 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 35.410 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 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 : 13.488 89.975 12491 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/Z covalent geometry : bond 0.00511 / 0.26 (36349) covalent geometry : angle 0.93168 / 0.51 (49459) SS BOND : bond 0.00862 / 0.35 ( 48) SS BOND : angle 1.78070 / 1.28 ( 96) hydrogen bonds : bond 0.22848 / 15.29 ( 735) hydrogen bonds : angle 9.56816 / 6.67 ( 1944) Misc. bond : bond 0.00082 / 0.06 ( 2) link_ALPHA1-3 : bond 0.00879 / 0.50 ( 5) link_ALPHA1-3 : angle 2.51558 / 1.72 ( 15) link_ALPHA1-6 : bond 0.00697 / 0.44 ( 8) link_ALPHA1-6 : angle 2.91819 / 2.04 ( 24) link_BETA1-2 : bond 0.00544 / 0.36 ( 1) link_BETA1-2 : angle 1.21681 / 0.92 ( 3) link_BETA1-4 : bond 0.00969 / 0.68 ( 36) link_BETA1-4 : angle 3.53728 / 2.52 ( 108) link_BETA1-6 : bond 0.00619 / 0.36 ( 5) link_BETA1-6 : angle 1.35244 / 0.84 ( 15) link_NAG-ASN : bond 0.01344 / 0.57 ( 43) link_NAG-ASN : angle 5.00467 / 3.48 ( 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 : 1.283 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: 0.2048 time to fit residues: 177.1940 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 : 1.365 ------------------------------------------------------------------------------- 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... ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.161500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.128037 restraints weight = 119199.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.131165 restraints weight = 81884.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.133474 restraints weight = 58700.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.134521 restraints weight = 43095.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.134952 restraints weight = 36857.835| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.123 36497 Z= 0.299 Angle : 0.927 19.409 49849 Z= 0.465 Chirality : 0.054 0.421 5919 Planarity : 0.007 0.079 6211 Dihedral : 6.886 29.305 4749 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 28.46 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.95 % Favored : 86.89 % Rotamer: Outliers : 0.50 % Allowed : 8.52 % Favored : 90.98 % 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: 679 sheet: -1.80 (0.21), residues: 572 loop : -2.74 (0.10), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 577 TYR 0.032 0.003 TYR E 707 PHE 0.026 0.003 PHE A 238 TRP 0.026 0.003 TRP A 436 HIS 0.015 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.30 (36349) covalent geometry : angle 0.88705 / 0.46 (49459) SS BOND : bond 0.00604 / 0.37 ( 48) SS BOND : angle 1.40819 / 0.91 ( 96) hydrogen bonds : bond 0.06902 / 4.66 ( 735) hydrogen bonds : angle 8.12768 / 5.62 ( 1944) Misc. bond : bond 0.00133 / 0.09 ( 2) link_ALPHA1-3 : bond 0.01143 / 0.69 ( 5) link_ALPHA1-3 : angle 3.00813 / 2.09 ( 15) link_ALPHA1-6 : bond 0.00907 / 0.51 ( 8) link_ALPHA1-6 : angle 2.06768 / 1.29 ( 24) link_BETA1-2 : bond 0.00385 / 0.26 ( 1) link_BETA1-2 : angle 1.38309 / 1.00 ( 3) link_BETA1-4 : bond 0.01102 / 0.64 ( 36) link_BETA1-4 : angle 2.87296 / 1.97 ( 108) link_BETA1-6 : bond 0.00678 / 0.40 ( 5) link_BETA1-6 : angle 1.54958 / 0.89 ( 15) link_NAG-ASN : bond 0.00827 / 0.51 ( 43) link_NAG-ASN : angle 4.45251 / 3.19 ( 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 522 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 503 time to evaluate : 1.377 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 131 CYS cc_start: 0.4551 (OUTLIER) cc_final: 0.3907 (p) REVERT: A 220 PHE cc_start: 0.8151 (p90) cc_final: 0.7823 (p90) REVERT: A 298 GLU cc_start: 0.8784 (tp30) cc_final: 0.8464 (tp30) REVERT: A 314 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7376 (tm-30) REVERT: A 740 MET cc_start: 0.7084 (tpt) cc_final: 0.6866 (tpt) REVERT: A 814 LYS cc_start: 0.7166 (mmtt) cc_final: 0.6934 (mmtt) REVERT: A 953 ASN cc_start: 0.8245 (m110) cc_final: 0.8042 (m110) REVERT: A 960 ASN cc_start: 0.9306 (t0) cc_final: 0.9101 (t0) REVERT: A 993 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7587 (mp) REVERT: A 1005 GLN cc_start: 0.8774 (tp40) cc_final: 0.8241 (tp-100) REVERT: A 1009 THR cc_start: 0.9206 (m) cc_final: 0.8833 (m) REVERT: A 1079 PRO cc_start: 0.7082 (Cg_endo) cc_final: 0.6834 (Cg_exo) REVERT: C 80 ASP cc_start: 0.8416 (t0) cc_final: 0.8094 (t0) REVERT: C 354 ASN cc_start: 0.9480 (t0) cc_final: 0.9038 (t0) REVERT: C 697 MET cc_start: 0.8610 (tmm) cc_final: 0.8380 (tmm) REVERT: C 790 LYS cc_start: 0.8120 (mmpt) cc_final: 0.7775 (mmmt) REVERT: C 817 PHE cc_start: 0.8591 (t80) cc_final: 0.8197 (t80) REVERT: C 900 MET cc_start: 0.3819 (mpp) cc_final: 0.3235 (mpp) REVERT: C 957 GLN cc_start: 0.8978 (tm-30) cc_final: 0.8659 (tm-30) REVERT: C 995 ARG cc_start: 0.8932 (pmt-80) cc_final: 0.8540 (pmt-80) REVERT: C 996 LEU cc_start: 0.8469 (mm) cc_final: 0.7491 (mm) REVERT: C 1018 ILE cc_start: 0.9347 (mt) cc_final: 0.8824 (mt) REVERT: C 1052 PHE cc_start: 0.8548 (m-10) cc_final: 0.7214 (m-10) REVERT: C 1103 PHE cc_start: 0.8345 (m-10) cc_final: 0.8061 (m-80) REVERT: C 1110 TYR cc_start: 0.8721 (t80) cc_final: 0.8491 (t80) REVERT: E 53 ASP cc_start: 0.6845 (t70) cc_final: 0.6545 (t70) REVERT: E 205 SER cc_start: 0.7189 (p) cc_final: 0.6871 (m) REVERT: E 328 ARG cc_start: 0.7108 (mmm160) cc_final: 0.6726 (mmm160) REVERT: E 737 ASP cc_start: 0.8242 (p0) cc_final: 0.7704 (p0) REVERT: E 800 PHE cc_start: 0.7424 (m-80) cc_final: 0.6695 (m-80) REVERT: E 923 ILE cc_start: 0.9469 (mt) cc_final: 0.9241 (mt) REVERT: E 925 ASN cc_start: 0.8948 (m110) cc_final: 0.8647 (m-40) REVERT: E 926 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8501 (tp-100) REVERT: E 949 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.9066 (pm20) REVERT: E 950 ASP cc_start: 0.8311 (m-30) cc_final: 0.7644 (m-30) REVERT: E 957 GLN cc_start: 0.9205 (pp30) cc_final: 0.8961 (pp30) REVERT: E 1007 TYR cc_start: 0.8155 (t80) cc_final: 0.7469 (t80) REVERT: E 1019 ARG cc_start: 0.8375 (tmt170) cc_final: 0.7898 (tmt170) REVERT: D 11 MET cc_start: 0.6666 (mmp) cc_final: 0.6453 (mmt) REVERT: F 21 MET cc_start: 0.6633 (mpp) cc_final: 0.6372 (mpp) REVERT: F 41 TRP cc_start: 0.5154 (m100) cc_final: 0.4598 (m100) REVERT: H 47 TRP cc_start: 0.6039 (t60) cc_final: 0.4812 (t60) REVERT: H 81 MET cc_start: -0.0843 (ttp) cc_final: -0.1381 (ttp) REVERT: K 101 TYR cc_start: 0.7480 (p90) cc_final: 0.7103 (p90) REVERT: L 4 MET cc_start: 0.4139 (mtp) cc_final: 0.0888 (mpp) REVERT: L 42 TYR cc_start: 0.6575 (m-80) cc_final: 0.6347 (m-80) REVERT: L 109 LYS cc_start: 0.6911 (tttt) cc_final: 0.6244 (tptt) outliers start: 19 outliers final: 5 residues processed: 519 average time/residue: 0.1998 time to fit residues: 174.2835 Evaluate side-chains 413 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 404 time to evaluate : 1.181 ------------------------------------------------------------------------------- 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: 0.9990 chunk 128 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 223 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 156 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 474 GLN ** 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 E 121 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 130 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 = 0.4444 r_free = 0.4444 target = 0.168266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.134574 restraints weight = 124537.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.137410 restraints weight = 85395.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.138994 restraints weight = 65813.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.140709 restraints weight = 48627.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.141706 restraints weight = 39321.338| |-----------------------------------------------------------------------------| r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.1616 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= 0.157 Angle : 0.789 18.933 49849 Z= 0.388 Chirality : 0.051 0.377 5919 Planarity : 0.006 0.083 6211 Dihedral : 6.422 32.152 4749 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.58 % Favored : 89.31 % Rotamer: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.34 % 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: -3.18 (0.11), residues: 4377 helix: -1.24 (0.18), residues: 677 sheet: -1.68 (0.21), residues: 559 loop : -2.60 (0.10), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.030 0.002 TYR C 873 PHE 0.024 0.002 PHE C 65 TRP 0.019 0.002 TRP C 436 HIS 0.010 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (36349) covalent geometry : angle 0.74942 / 0.38 (49459) SS BOND : bond 0.00378 / 0.25 ( 48) SS BOND : angle 1.30600 / 0.84 ( 96) hydrogen bonds : bond 0.05700 / 3.82 ( 735) hydrogen bonds : angle 7.53949 / 5.20 ( 1944) Misc. bond : bond 0.00079 / 0.05 ( 2) link_ALPHA1-3 : bond 0.01141 / 0.69 ( 5) link_ALPHA1-3 : angle 2.65381 / 1.82 ( 15) link_ALPHA1-6 : bond 0.00592 / 0.34 ( 8) link_ALPHA1-6 : angle 1.78985 / 1.13 ( 24) link_BETA1-2 : bond 0.00880 / 0.59 ( 1) link_BETA1-2 : angle 1.37730 / 0.99 ( 3) link_BETA1-4 : bond 0.00929 / 0.65 ( 36) link_BETA1-4 : angle 2.64315 / 1.79 ( 108) link_BETA1-6 : bond 0.00713 / 0.42 ( 5) link_BETA1-6 : angle 1.16674 / 0.72 ( 15) link_NAG-ASN : bond 0.00686 / 0.43 ( 43) link_NAG-ASN : angle 4.09736 / 2.92 ( 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 560 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 555 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8036 (mmp-170) cc_final: 0.6782 (mmp-170) REVERT: A 220 PHE cc_start: 0.8063 (p90) cc_final: 0.7762 (p90) REVERT: A 298 GLU cc_start: 0.8646 (tp30) cc_final: 0.8304 (tp30) REVERT: A 312 ILE cc_start: 0.8873 (pt) cc_final: 0.8666 (pt) REVERT: A 314 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7249 (tm-30) REVERT: A 817 PHE cc_start: 0.8111 (t80) cc_final: 0.7841 (t80) REVERT: A 993 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7394 (mt) REVERT: A 1005 GLN cc_start: 0.8506 (tp40) cc_final: 0.7919 (tp-100) REVERT: A 1009 THR cc_start: 0.9101 (m) cc_final: 0.8630 (m) REVERT: C 53 ASP cc_start: 0.7791 (t70) cc_final: 0.7203 (t70) REVERT: C 80 ASP cc_start: 0.8433 (t0) cc_final: 0.8054 (t0) REVERT: C 354 ASN cc_start: 0.9433 (t0) cc_final: 0.9118 (t0) REVERT: C 498 GLN cc_start: 0.8384 (mm110) cc_final: 0.8103 (mm-40) REVERT: C 790 LYS cc_start: 0.7959 (mmpt) cc_final: 0.7603 (mmmt) REVERT: C 808 ASP cc_start: 0.9057 (t70) cc_final: 0.8813 (t0) REVERT: C 817 PHE cc_start: 0.8360 (t80) cc_final: 0.7979 (t80) REVERT: C 901 GLN cc_start: 0.8579 (pp30) cc_final: 0.8305 (pp30) REVERT: C 990 GLU cc_start: 0.8049 (tp30) cc_final: 0.7814 (mm-30) REVERT: C 996 LEU cc_start: 0.8502 (mm) cc_final: 0.8216 (mm) REVERT: C 1018 ILE cc_start: 0.9266 (mt) cc_final: 0.8726 (mt) REVERT: C 1052 PHE cc_start: 0.8381 (m-10) cc_final: 0.6912 (m-10) REVERT: C 1103 PHE cc_start: 0.8260 (m-10) cc_final: 0.7972 (m-80) REVERT: C 1110 TYR cc_start: 0.8615 (t80) cc_final: 0.8375 (t80) REVERT: E 53 ASP cc_start: 0.6740 (t70) cc_final: 0.6460 (t70) REVERT: E 205 SER cc_start: 0.7181 (p) cc_final: 0.6729 (m) REVERT: E 328 ARG cc_start: 0.7019 (mmm160) cc_final: 0.6693 (mmm160) REVERT: E 737 ASP cc_start: 0.8003 (p0) cc_final: 0.7436 (p0) REVERT: E 800 PHE cc_start: 0.7228 (m-80) cc_final: 0.6510 (m-80) REVERT: E 925 ASN cc_start: 0.8877 (m110) cc_final: 0.8463 (m-40) REVERT: E 950 ASP cc_start: 0.8237 (m-30) cc_final: 0.7686 (m-30) REVERT: E 1007 TYR cc_start: 0.7893 (t80) cc_final: 0.7150 (t80) REVERT: E 1010 GLN cc_start: 0.8303 (tp40) cc_final: 0.7967 (tp-100) REVERT: E 1050 MET cc_start: 0.7935 (ppp) cc_final: 0.7565 (ppp) REVERT: E 1101 HIS cc_start: 0.6750 (m90) cc_final: 0.6186 (m90) REVERT: E 1121 PHE cc_start: 0.6857 (p90) cc_final: 0.6436 (p90) REVERT: H 47 TRP cc_start: 0.5966 (t60) cc_final: 0.4997 (t60) REVERT: L 4 MET cc_start: 0.4878 (mtp) cc_final: 0.1609 (mpp) REVERT: L 109 LYS cc_start: 0.6825 (tttt) cc_final: 0.6483 (ptmt) outliers start: 5 outliers final: 1 residues processed: 558 average time/residue: 0.2010 time to fit residues: 187.4893 Evaluate side-chains 435 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 433 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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: 6.9990 chunk 285 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 chunk 365 optimal weight: 50.0000 chunk 431 optimal weight: 5.9990 chunk 222 optimal weight: 4.9990 chunk 407 optimal weight: 40.0000 chunk 186 optimal weight: 0.9990 chunk 234 optimal weight: 0.9990 chunk 148 optimal weight: 10.0000 chunk 434 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN A 960 ASN A 969 ASN ** 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 ** C 969 ASN ** 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 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 955 ASN ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 GLN I 130 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.166424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.132337 restraints weight = 120027.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.135547 restraints weight = 81196.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.138024 restraints weight = 57619.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.139526 restraints weight = 41568.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.139643 restraints weight = 36873.571| |-----------------------------------------------------------------------------| r_work (final): 0.4080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 36497 Z= 0.192 Angle : 0.798 19.274 49849 Z= 0.395 Chirality : 0.050 0.385 5919 Planarity : 0.006 0.084 6211 Dihedral : 6.407 29.249 4749 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 21.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.15 % Favored : 87.73 % Rotamer: Outliers : 0.16 % Allowed : 4.38 % Favored : 95.47 % 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: -3.18 (0.12), residues: 4377 helix: -1.26 (0.18), residues: 681 sheet: -1.69 (0.21), residues: 554 loop : -2.59 (0.10), residues: 3142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 995 TYR 0.025 0.002 TYR A 873 PHE 0.025 0.002 PHE H 29 TRP 0.018 0.002 TRP C 436 HIS 0.010 0.002 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (36349) covalent geometry : angle 0.75913 / 0.39 (49459) SS BOND : bond 0.00435 / 0.29 ( 48) SS BOND : angle 1.14855 / 0.75 ( 96) hydrogen bonds : bond 0.05723 / 3.86 ( 735) hydrogen bonds : angle 7.48254 / 5.16 ( 1944) Misc. bond : bond 0.00071 / 0.05 ( 2) link_ALPHA1-3 : bond 0.01255 / 0.71 ( 5) link_ALPHA1-3 : angle 2.64628 / 1.81 ( 15) link_ALPHA1-6 : bond 0.00464 / 0.25 ( 8) link_ALPHA1-6 : angle 1.75867 / 1.07 ( 24) link_BETA1-2 : bond 0.00673 / 0.45 ( 1) link_BETA1-2 : angle 1.28226 / 0.93 ( 3) link_BETA1-4 : bond 0.00838 / 0.58 ( 36) link_BETA1-4 : angle 2.49691 / 1.62 ( 108) link_BETA1-6 : bond 0.00683 / 0.40 ( 5) link_BETA1-6 : angle 1.24398 / 0.73 ( 15) link_NAG-ASN : bond 0.00661 / 0.41 ( 43) link_NAG-ASN : angle 4.18149 / 2.99 ( 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 536 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 530 time to evaluate : 1.192 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 88 ASP cc_start: 0.7984 (m-30) cc_final: 0.7781 (m-30) REVERT: A 131 CYS cc_start: 0.4860 (OUTLIER) cc_final: 0.4262 (p) REVERT: A 220 PHE cc_start: 0.8062 (p90) cc_final: 0.7723 (p90) REVERT: A 298 GLU cc_start: 0.8684 (tp30) cc_final: 0.8375 (tp30) REVERT: A 312 ILE cc_start: 0.8851 (pt) cc_final: 0.8643 (pt) REVERT: A 314 GLN cc_start: 0.7865 (tm-30) cc_final: 0.7306 (tm-30) REVERT: A 817 PHE cc_start: 0.8246 (t80) cc_final: 0.7947 (t80) REVERT: A 960 ASN cc_start: 0.8964 (m110) cc_final: 0.8760 (t0) REVERT: A 1010 GLN cc_start: 0.8285 (mp10) cc_final: 0.7894 (mp10) REVERT: A 1064 HIS cc_start: 0.8408 (m170) cc_final: 0.7858 (m170) REVERT: C 44 ARG cc_start: 0.8754 (ptt-90) cc_final: 0.8514 (ptt180) REVERT: C 80 ASP cc_start: 0.8435 (t0) cc_final: 0.8014 (t0) REVERT: C 354 ASN cc_start: 0.9446 (t0) cc_final: 0.9140 (t0) REVERT: C 396 TYR cc_start: 0.8654 (m-80) cc_final: 0.8378 (m-80) REVERT: C 790 LYS cc_start: 0.7935 (mmpt) cc_final: 0.7610 (mmmt) REVERT: C 808 ASP cc_start: 0.9021 (t70) cc_final: 0.8801 (t0) REVERT: C 817 PHE cc_start: 0.8349 (t80) cc_final: 0.8010 (t80) REVERT: C 883 THR cc_start: 0.7767 (p) cc_final: 0.7548 (p) REVERT: C 900 MET cc_start: 0.3835 (mpp) cc_final: 0.3326 (mpp) REVERT: C 990 GLU cc_start: 0.8138 (tp30) cc_final: 0.7861 (mm-30) REVERT: C 996 LEU cc_start: 0.8427 (mm) cc_final: 0.8163 (mm) REVERT: C 1018 ILE cc_start: 0.9334 (mt) cc_final: 0.8853 (mt) REVERT: C 1052 PHE cc_start: 0.8421 (m-10) cc_final: 0.7248 (m-10) REVERT: C 1103 PHE cc_start: 0.8259 (m-10) cc_final: 0.8000 (m-80) REVERT: C 1110 TYR cc_start: 0.8616 (t80) cc_final: 0.8360 (t80) REVERT: C 1114 ILE cc_start: 0.8291 (mm) cc_final: 0.7929 (tp) REVERT: E 53 ASP cc_start: 0.6992 (t70) cc_final: 0.6623 (t70) REVERT: E 205 SER cc_start: 0.7223 (p) cc_final: 0.6767 (m) REVERT: E 328 ARG cc_start: 0.7159 (mmm160) cc_final: 0.6680 (mmm160) REVERT: E 737 ASP cc_start: 0.8093 (p0) cc_final: 0.7550 (p0) REVERT: E 800 PHE cc_start: 0.7311 (m-80) cc_final: 0.6578 (m-80) REVERT: E 925 ASN cc_start: 0.8962 (m110) cc_final: 0.8549 (m-40) REVERT: E 950 ASP cc_start: 0.8368 (m-30) cc_final: 0.7848 (m-30) REVERT: E 962 LEU cc_start: 0.9325 (tp) cc_final: 0.9106 (tp) REVERT: E 1007 TYR cc_start: 0.8078 (t80) cc_final: 0.7350 (t80) REVERT: E 1101 HIS cc_start: 0.6996 (m90) cc_final: 0.6218 (m90) REVERT: E 1121 PHE cc_start: 0.6733 (p90) cc_final: 0.6461 (p90) REVERT: F 41 TRP cc_start: 0.5066 (m100) cc_final: 0.4856 (m100) REVERT: H 47 TRP cc_start: 0.6033 (t60) cc_final: 0.4844 (t60) REVERT: K 81 MET cc_start: 0.4256 (tpt) cc_final: 0.3587 (tpt) REVERT: L 4 MET cc_start: 0.4823 (mtp) cc_final: 0.1437 (mpp) REVERT: L 42 TYR cc_start: 0.5935 (m-80) cc_final: 0.5572 (m-80) REVERT: L 109 LYS cc_start: 0.6917 (tttt) cc_final: 0.6610 (ptmt) outliers start: 6 outliers final: 0 residues processed: 532 average time/residue: 0.1978 time to fit residues: 175.6396 Evaluate side-chains 413 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 412 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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: 4.9990 chunk 228 optimal weight: 4.9990 chunk 412 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 362 optimal weight: 2.9990 chunk 371 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 183 optimal weight: 0.9980 chunk 250 optimal weight: 20.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 437 ASN ** A 901 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 762 GLN C 856 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN ** 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 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 D 62 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.167849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.132077 restraints weight = 122126.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.135446 restraints weight = 80909.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.137566 restraints weight = 58287.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.139329 restraints weight = 46227.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.140574 restraints weight = 38745.657| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 36497 Z= 0.162 Angle : 0.770 18.986 49849 Z= 0.380 Chirality : 0.050 0.453 5919 Planarity : 0.006 0.089 6211 Dihedral : 6.253 33.167 4749 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.99 % Favored : 88.90 % Rotamer: Outliers : 0.18 % Allowed : 3.47 % Favored : 96.35 % 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: -3.10 (0.12), residues: 4377 helix: -1.12 (0.18), residues: 678 sheet: -1.74 (0.21), residues: 575 loop : -2.53 (0.10), residues: 3124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 995 TYR 0.029 0.002 TYR A 873 PHE 0.040 0.002 PHE E1089 TRP 0.022 0.002 TRP L 41 HIS 0.009 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 (36349) covalent geometry : angle 0.73321 / 0.37 (49459) SS BOND : bond 0.00349 / 0.24 ( 48) SS BOND : angle 1.29682 / 0.80 ( 96) hydrogen bonds : bond 0.05304 / 3.56 ( 735) hydrogen bonds : angle 7.23955 / 4.99 ( 1944) Misc. bond : bond 0.00069 / 0.05 ( 2) link_ALPHA1-3 : bond 0.01134 / 0.66 ( 5) link_ALPHA1-3 : angle 2.50298 / 1.71 ( 15) link_ALPHA1-6 : bond 0.00446 / 0.25 ( 8) link_ALPHA1-6 : angle 1.68841 / 1.04 ( 24) link_BETA1-2 : bond 0.00771 / 0.51 ( 1) link_BETA1-2 : angle 1.25599 / 0.92 ( 3) link_BETA1-4 : bond 0.00806 / 0.56 ( 36) link_BETA1-4 : angle 2.39041 / 1.52 ( 108) link_BETA1-6 : bond 0.00672 / 0.40 ( 5) link_BETA1-6 : angle 1.18583 / 0.72 ( 15) link_NAG-ASN : bond 0.00625 / 0.39 ( 43) link_NAG-ASN : angle 3.94835 / 2.82 ( 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 541 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 534 time to evaluate : 1.247 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: 0.8028 (p90) cc_final: 0.7760 (p90) REVERT: A 298 GLU cc_start: 0.8665 (tp30) cc_final: 0.8360 (tp30) REVERT: A 314 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7534 (tm-30) REVERT: A 817 PHE cc_start: 0.8133 (t80) cc_final: 0.7881 (t80) REVERT: A 900 MET cc_start: 0.7380 (mpp) cc_final: 0.6915 (mpp) REVERT: A 953 ASN cc_start: 0.8154 (m110) cc_final: 0.7896 (m110) REVERT: A 1064 HIS cc_start: 0.8373 (m170) cc_final: 0.7977 (m170) REVERT: C 80 ASP cc_start: 0.8419 (t0) cc_final: 0.7944 (t0) REVERT: C 354 ASN cc_start: 0.9473 (t0) cc_final: 0.9205 (t0) REVERT: C 396 TYR cc_start: 0.8593 (m-80) cc_final: 0.8134 (m-80) REVERT: C 790 LYS cc_start: 0.7897 (mmpt) cc_final: 0.7602 (mmmt) REVERT: C 808 ASP cc_start: 0.9041 (t70) cc_final: 0.8831 (t0) REVERT: C 900 MET cc_start: 0.4191 (mpp) cc_final: 0.3617 (mpp) REVERT: C 926 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8545 (pm20) REVERT: C 996 LEU cc_start: 0.8421 (mm) cc_final: 0.8183 (mm) REVERT: C 1052 PHE cc_start: 0.8591 (m-10) cc_final: 0.7381 (m-10) REVERT: C 1103 PHE cc_start: 0.8168 (m-10) cc_final: 0.7903 (m-80) REVERT: C 1110 TYR cc_start: 0.8574 (t80) cc_final: 0.8322 (t80) REVERT: C 1114 ILE cc_start: 0.8118 (mm) cc_final: 0.7743 (tp) REVERT: E 53 ASP cc_start: 0.7189 (t70) cc_final: 0.6814 (t70) REVERT: E 104 TRP cc_start: 0.5467 (m100) cc_final: 0.5213 (m100) REVERT: E 106 PHE cc_start: 0.6473 (m-10) cc_final: 0.6153 (m-10) REVERT: E 205 SER cc_start: 0.7350 (p) cc_final: 0.6800 (m) REVERT: E 328 ARG cc_start: 0.7112 (mmm160) cc_final: 0.6635 (mmm160) REVERT: E 737 ASP cc_start: 0.8046 (p0) cc_final: 0.7530 (p0) REVERT: E 800 PHE cc_start: 0.7192 (m-80) cc_final: 0.6568 (m-80) REVERT: E 918 GLU cc_start: 0.8971 (tt0) cc_final: 0.8620 (tm-30) REVERT: E 950 ASP cc_start: 0.8319 (m-30) cc_final: 0.7748 (m-30) REVERT: E 962 LEU cc_start: 0.9293 (tp) cc_final: 0.9085 (tp) REVERT: E 1007 TYR cc_start: 0.8022 (t80) cc_final: 0.7295 (t80) REVERT: E 1010 GLN cc_start: 0.8217 (tp40) cc_final: 0.7861 (tp40) REVERT: E 1050 MET cc_start: 0.7670 (ppp) cc_final: 0.7361 (ppp) REVERT: E 1121 PHE cc_start: 0.6483 (p90) cc_final: 0.6186 (p90) REVERT: F 41 TRP cc_start: 0.5131 (m100) cc_final: 0.4859 (m100) REVERT: H 47 TRP cc_start: 0.5950 (t60) cc_final: 0.5015 (t60) REVERT: I 98 TYR cc_start: 0.8629 (t80) cc_final: 0.8091 (t80) REVERT: K 81 MET cc_start: 0.4078 (tpt) cc_final: 0.3481 (tpt) REVERT: L 4 MET cc_start: 0.4924 (mtp) cc_final: 0.2045 (mpp) REVERT: L 42 TYR cc_start: 0.6049 (m-80) cc_final: 0.5559 (m-80) REVERT: L 109 LYS cc_start: 0.6642 (tttt) cc_final: 0.6345 (ptmt) outliers start: 7 outliers final: 1 residues processed: 538 average time/residue: 0.2065 time to fit residues: 186.5453 Evaluate side-chains 417 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 415 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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: 9.9990 chunk 49 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 358 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 385 optimal weight: 0.0170 chunk 342 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 117 optimal weight: 6.9990 overall best weight: 3.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A 957 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 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 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** ** C1036 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 439 ASN ** E 606 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** 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** F 96 GLN K 6 GLN ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 205 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.166518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.133174 restraints weight = 121188.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.136641 restraints weight = 79049.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.139007 restraints weight = 56203.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.139893 restraints weight = 41754.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.140694 restraints weight = 36406.029| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6535 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 36497 Z= 0.182 Angle : 0.794 19.097 49849 Z= 0.391 Chirality : 0.051 0.384 5919 Planarity : 0.006 0.134 6211 Dihedral : 6.291 31.577 4749 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.90 % Favored : 87.98 % Rotamer: Outliers : 0.10 % Allowed : 3.02 % Favored : 96.87 % 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: -3.14 (0.12), residues: 4377 helix: -1.22 (0.18), residues: 671 sheet: -1.80 (0.20), residues: 604 loop : -2.52 (0.10), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 995 TYR 0.029 0.002 TYR A 873 PHE 0.025 0.002 PHE C 55 TRP 0.018 0.002 TRP C 436 HIS 0.010 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (36349) covalent geometry : angle 0.75646 / 0.38 (49459) SS BOND : bond 0.00401 / 0.26 ( 48) SS BOND : angle 1.24229 / 0.78 ( 96) hydrogen bonds : bond 0.05396 / 3.64 ( 735) hydrogen bonds : angle 7.28006 / 5.03 ( 1944) Misc. bond : bond 0.00086 / 0.06 ( 2) link_ALPHA1-3 : bond 0.01107 / 0.64 ( 5) link_ALPHA1-3 : angle 2.56296 / 1.76 ( 15) link_ALPHA1-6 : bond 0.00417 / 0.22 ( 8) link_ALPHA1-6 : angle 1.68424 / 1.02 ( 24) link_BETA1-2 : bond 0.00734 / 0.49 ( 1) link_BETA1-2 : angle 1.24955 / 0.92 ( 3) link_BETA1-4 : bond 0.00812 / 0.57 ( 36) link_BETA1-4 : angle 2.42485 / 1.53 ( 108) link_BETA1-6 : bond 0.00676 / 0.40 ( 5) link_BETA1-6 : angle 1.23140 / 0.74 ( 15) link_NAG-ASN : bond 0.00682 / 0.43 ( 43) link_NAG-ASN : angle 4.08638 / 2.89 ( 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 521 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 517 time to evaluate : 1.289 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: A 220 PHE cc_start: 0.8149 (p90) cc_final: 0.7783 (p90) REVERT: A 298 GLU cc_start: 0.8644 (tp30) cc_final: 0.8351 (tp30) REVERT: A 314 GLN cc_start: 0.7897 (tm-30) cc_final: 0.7470 (tm-30) REVERT: A 723 THR cc_start: 0.9008 (p) cc_final: 0.8550 (p) REVERT: A 814 LYS cc_start: 0.7101 (mmtt) cc_final: 0.6773 (mmpt) REVERT: A 817 PHE cc_start: 0.8228 (t80) cc_final: 0.7960 (t80) REVERT: A 1064 HIS cc_start: 0.8498 (m170) cc_final: 0.7726 (m170) REVERT: C 80 ASP cc_start: 0.8506 (t0) cc_final: 0.8027 (t0) REVERT: C 354 ASN cc_start: 0.9439 (t0) cc_final: 0.9171 (t0) REVERT: C 396 TYR cc_start: 0.8627 (m-80) cc_final: 0.8399 (m-80) REVERT: C 498 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8160 (mm110) REVERT: C 790 LYS cc_start: 0.7938 (mmpt) cc_final: 0.7565 (mmmt) REVERT: C 900 MET cc_start: 0.3698 (mpp) cc_final: 0.3209 (mpp) REVERT: C 902 MET cc_start: 0.8289 (pmm) cc_final: 0.7392 (pmm) REVERT: C 996 LEU cc_start: 0.8406 (mm) cc_final: 0.8186 (mm) REVERT: C 1018 ILE cc_start: 0.9300 (mt) cc_final: 0.8828 (mt) REVERT: C 1052 PHE cc_start: 0.8587 (m-10) cc_final: 0.7452 (m-10) REVERT: C 1103 PHE cc_start: 0.8166 (m-10) cc_final: 0.7884 (m-80) REVERT: C 1110 TYR cc_start: 0.8597 (t80) cc_final: 0.8334 (t80) REVERT: C 1114 ILE cc_start: 0.8195 (mm) cc_final: 0.7837 (tp) REVERT: E 53 ASP cc_start: 0.7184 (t70) cc_final: 0.6766 (t70) REVERT: E 104 TRP cc_start: 0.5453 (m100) cc_final: 0.5206 (m100) REVERT: E 106 PHE cc_start: 0.6522 (m-10) cc_final: 0.6253 (m-10) REVERT: E 205 SER cc_start: 0.7262 (p) cc_final: 0.6807 (m) REVERT: E 328 ARG cc_start: 0.7240 (mmm160) cc_final: 0.6769 (mmm-85) REVERT: E 737 ASP cc_start: 0.8057 (p0) cc_final: 0.7550 (p0) REVERT: E 800 PHE cc_start: 0.7223 (m-80) cc_final: 0.6579 (m-80) REVERT: E 918 GLU cc_start: 0.8985 (tt0) cc_final: 0.8656 (tm-30) REVERT: E 950 ASP cc_start: 0.8387 (m-30) cc_final: 0.7866 (m-30) REVERT: E 1007 TYR cc_start: 0.8126 (t80) cc_final: 0.7353 (t80) REVERT: E 1010 GLN cc_start: 0.8345 (tp40) cc_final: 0.7968 (tp-100) REVERT: E 1121 PHE cc_start: 0.6612 (p90) cc_final: 0.6378 (p90) REVERT: H 47 TRP cc_start: 0.6208 (t60) cc_final: 0.4961 (t60) REVERT: I 98 TYR cc_start: 0.8713 (t80) cc_final: 0.8172 (t80) REVERT: K 81 MET cc_start: 0.4241 (tpt) cc_final: 0.3418 (tpt) REVERT: L 4 MET cc_start: 0.4975 (mtp) cc_final: 0.2158 (mpp) REVERT: L 42 TYR cc_start: 0.5744 (m-80) cc_final: 0.5453 (m-80) REVERT: L 109 LYS cc_start: 0.6748 (tttt) cc_final: 0.6516 (ptmt) outliers start: 4 outliers final: 0 residues processed: 520 average time/residue: 0.2089 time to fit residues: 181.5849 Evaluate side-chains 410 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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: 5.9990 chunk 64 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 286 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 chunk 332 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 271 optimal weight: 0.6980 chunk 377 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 960 ASN A 969 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** 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 125 ASN C 185 ASN C 540 ASN C 762 GLN C 856 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1058 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.168449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.133933 restraints weight = 125264.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.137044 restraints weight = 83264.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.139412 restraints weight = 60233.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.140752 restraints weight = 46717.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.141882 restraints weight = 39369.160| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 36497 Z= 0.159 Angle : 0.787 18.854 49849 Z= 0.385 Chirality : 0.051 0.370 5919 Planarity : 0.006 0.101 6211 Dihedral : 6.166 34.111 4749 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 11.01 % Favored : 88.87 % Rotamer: Outliers : 0.13 % Allowed : 1.77 % Favored : 98.10 % 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: -3.09 (0.12), residues: 4377 helix: -1.17 (0.18), residues: 674 sheet: -1.81 (0.20), residues: 600 loop : -2.49 (0.10), residues: 3103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 995 TYR 0.033 0.002 TYR A 873 PHE 0.026 0.002 PHE E 275 TRP 0.029 0.002 TRP L 41 HIS 0.024 0.002 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (36349) covalent geometry : angle 0.74543 / 0.38 (49459) SS BOND : bond 0.00323 / 0.21 ( 48) SS BOND : angle 1.27560 / 0.80 ( 96) hydrogen bonds : bond 0.05175 / 3.47 ( 735) hydrogen bonds : angle 7.16290 / 4.96 ( 1944) Misc. bond : bond 0.00069 / 0.05 ( 2) link_ALPHA1-3 : bond 0.01055 / 0.62 ( 5) link_ALPHA1-3 : angle 2.45511 / 1.68 ( 15) link_ALPHA1-6 : bond 0.00434 / 0.24 ( 8) link_ALPHA1-6 : angle 1.63859 / 1.01 ( 24) link_BETA1-2 : bond 0.00782 / 0.52 ( 1) link_BETA1-2 : angle 1.27051 / 0.93 ( 3) link_BETA1-4 : bond 0.00777 / 0.55 ( 36) link_BETA1-4 : angle 2.34238 / 1.46 ( 108) link_BETA1-6 : bond 0.00673 / 0.40 ( 5) link_BETA1-6 : angle 1.17781 / 0.72 ( 15) link_NAG-ASN : bond 0.00717 / 0.47 ( 43) link_NAG-ASN : angle 4.36139 / 3.09 ( 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 529 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 524 time to evaluate : 1.610 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: A 88 ASP cc_start: 0.7847 (m-30) cc_final: 0.7647 (m-30) REVERT: A 220 PHE cc_start: 0.7997 (p90) cc_final: 0.7792 (p90) REVERT: A 298 GLU cc_start: 0.8586 (tp30) cc_final: 0.8257 (tp30) REVERT: A 314 GLN cc_start: 0.7826 (tm-30) cc_final: 0.7367 (tm-30) REVERT: A 953 ASN cc_start: 0.8217 (m110) cc_final: 0.8004 (m110) REVERT: C 80 ASP cc_start: 0.8393 (t0) cc_final: 0.7890 (t0) REVERT: C 354 ASN cc_start: 0.9496 (t0) cc_final: 0.9258 (t0) REVERT: C 396 TYR cc_start: 0.8517 (m-80) cc_final: 0.8093 (m-80) REVERT: C 818 ILE cc_start: 0.9396 (pt) cc_final: 0.9177 (pt) REVERT: C 900 MET cc_start: 0.4029 (mpp) cc_final: 0.3453 (mpp) REVERT: C 902 MET cc_start: 0.8309 (pmm) cc_final: 0.7096 (pmm) REVERT: C 916 LEU cc_start: 0.6968 (tp) cc_final: 0.6687 (tp) REVERT: C 1018 ILE cc_start: 0.9252 (mt) cc_final: 0.8695 (mt) REVERT: C 1050 MET cc_start: 0.7351 (ttt) cc_final: 0.6461 (ttt) REVERT: C 1052 PHE cc_start: 0.8543 (m-10) cc_final: 0.7098 (m-10) REVERT: C 1114 ILE cc_start: 0.7930 (mm) cc_final: 0.7596 (tp) REVERT: E 53 ASP cc_start: 0.7051 (t70) cc_final: 0.6622 (t70) REVERT: E 104 TRP cc_start: 0.5437 (m100) cc_final: 0.5197 (m100) REVERT: E 106 PHE cc_start: 0.6468 (m-10) cc_final: 0.6202 (m-10) REVERT: E 205 SER cc_start: 0.7299 (p) cc_final: 0.6859 (m) REVERT: E 328 ARG cc_start: 0.7139 (mmm160) cc_final: 0.6719 (mmm160) REVERT: E 645 THR cc_start: 0.9059 (p) cc_final: 0.8556 (t) REVERT: E 737 ASP cc_start: 0.7935 (p0) cc_final: 0.7508 (p0) REVERT: E 800 PHE cc_start: 0.6957 (m-80) cc_final: 0.6426 (m-80) REVERT: E 918 GLU cc_start: 0.8834 (tt0) cc_final: 0.8369 (tm-30) REVERT: E 926 GLN cc_start: 0.9215 (pm20) cc_final: 0.8772 (pm20) REVERT: E 950 ASP cc_start: 0.8279 (m-30) cc_final: 0.7754 (m-30) REVERT: E 962 LEU cc_start: 0.9178 (tp) cc_final: 0.8956 (tp) REVERT: E 1007 TYR cc_start: 0.7857 (t80) cc_final: 0.7059 (t80) REVERT: E 1010 GLN cc_start: 0.7976 (tp40) cc_final: 0.7668 (tp-100) REVERT: E 1050 MET cc_start: 0.7847 (ppp) cc_final: 0.7554 (ppp) REVERT: E 1121 PHE cc_start: 0.6064 (p90) cc_final: 0.5797 (p90) REVERT: H 47 TRP cc_start: 0.6112 (t60) cc_final: 0.4889 (t60) REVERT: I 98 TYR cc_start: 0.8497 (t80) cc_final: 0.8068 (t80) REVERT: K 81 MET cc_start: 0.4004 (tpt) cc_final: 0.3504 (tpt) REVERT: L 4 MET cc_start: 0.4829 (mtp) cc_final: 0.2037 (mpp) REVERT: L 42 TYR cc_start: 0.5796 (m-80) cc_final: 0.5331 (m-80) REVERT: L 109 LYS cc_start: 0.6739 (tttt) cc_final: 0.6241 (tptt) outliers start: 5 outliers final: 0 residues processed: 529 average time/residue: 0.2111 time to fit residues: 187.0169 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 : 1.303 ------------------------------------------------------------------------------- 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: 9.9990 chunk 421 optimal weight: 2.9990 chunk 309 optimal weight: 8.9990 chunk 425 optimal weight: 6.9990 chunk 54 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 45 optimal weight: 0.0870 chunk 361 optimal weight: 30.0000 chunk 75 optimal weight: 2.9990 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 437 ASN ** 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** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.170053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.137109 restraints weight = 124630.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.140067 restraints weight = 82499.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.142509 restraints weight = 60692.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.143498 restraints weight = 45898.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.144185 restraints weight = 38211.586| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2502 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= 0.143 Angle : 0.765 18.899 49849 Z= 0.376 Chirality : 0.050 0.366 5919 Planarity : 0.006 0.100 6211 Dihedral : 6.016 33.130 4749 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.94 % Favored : 88.94 % Rotamer: Outliers : 0.08 % Allowed : 1.62 % Favored : 98.31 % 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: -3.02 (0.12), residues: 4377 helix: -1.09 (0.19), residues: 675 sheet: -1.75 (0.21), residues: 602 loop : -2.45 (0.11), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 995 TYR 0.034 0.002 TYR A 873 PHE 0.030 0.002 PHE H 29 TRP 0.018 0.002 TRP C 436 HIS 0.019 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (36349) covalent geometry : angle 0.73043 / 0.37 (49459) SS BOND : bond 0.00367 / 0.25 ( 48) SS BOND : angle 1.19987 / 0.76 ( 96) hydrogen bonds : bond 0.04870 / 3.30 ( 735) hydrogen bonds : angle 7.05092 / 4.88 ( 1944) Misc. bond : bond 0.00067 / 0.04 ( 2) link_ALPHA1-3 : bond 0.01076 / 0.62 ( 5) link_ALPHA1-3 : angle 2.40058 / 1.64 ( 15) link_ALPHA1-6 : bond 0.00433 / 0.24 ( 8) link_ALPHA1-6 : angle 1.60744 / 0.99 ( 24) link_BETA1-2 : bond 0.00781 / 0.52 ( 1) link_BETA1-2 : angle 1.24314 / 0.92 ( 3) link_BETA1-4 : bond 0.00794 / 0.56 ( 36) link_BETA1-4 : angle 2.27576 / 1.40 ( 108) link_BETA1-6 : bond 0.00656 / 0.39 ( 5) link_BETA1-6 : angle 1.15965 / 0.72 ( 15) link_NAG-ASN : bond 0.00663 / 0.43 ( 43) link_NAG-ASN : angle 3.85644 / 2.75 ( 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 530 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 527 time to evaluate : 1.051 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 92 PHE cc_start: 0.6865 (t80) cc_final: 0.6523 (t80) REVERT: A 220 PHE cc_start: 0.8041 (p90) cc_final: 0.7780 (p90) REVERT: A 298 GLU cc_start: 0.8582 (tp30) cc_final: 0.8266 (tp30) REVERT: A 314 GLN cc_start: 0.7827 (tm-30) cc_final: 0.7340 (tm-30) REVERT: A 882 ILE cc_start: 0.9459 (mt) cc_final: 0.9235 (mt) REVERT: A 953 ASN cc_start: 0.8221 (m110) cc_final: 0.7921 (m110) REVERT: A 1017 GLU cc_start: 0.8231 (tm-30) cc_final: 0.8001 (tm-30) REVERT: A 1033 VAL cc_start: 0.8710 (t) cc_final: 0.8370 (t) REVERT: C 80 ASP cc_start: 0.8379 (t0) cc_final: 0.7923 (t0) REVERT: C 354 ASN cc_start: 0.9441 (t0) cc_final: 0.9120 (t0) REVERT: C 396 TYR cc_start: 0.8548 (m-80) cc_final: 0.8114 (m-80) REVERT: C 765 ARG cc_start: 0.8514 (mtp-110) cc_final: 0.8215 (ptm-80) REVERT: C 777 ASN cc_start: 0.8835 (m110) cc_final: 0.8602 (m110) REVERT: C 790 LYS cc_start: 0.8012 (mmpt) cc_final: 0.7599 (mmmt) REVERT: C 900 MET cc_start: 0.3737 (mpp) cc_final: 0.2656 (mpp) REVERT: C 902 MET cc_start: 0.8274 (pmm) cc_final: 0.7212 (pmm) REVERT: C 990 GLU cc_start: 0.7578 (mp0) cc_final: 0.7358 (mp0) REVERT: C 1018 ILE cc_start: 0.9252 (mt) cc_final: 0.8853 (mt) REVERT: C 1050 MET cc_start: 0.7158 (ttt) cc_final: 0.6446 (ttt) REVERT: C 1052 PHE cc_start: 0.8559 (m-10) cc_final: 0.7242 (m-10) REVERT: C 1103 PHE cc_start: 0.7966 (m-80) cc_final: 0.7624 (m-80) REVERT: C 1114 ILE cc_start: 0.8015 (mm) cc_final: 0.7652 (tp) REVERT: E 53 ASP cc_start: 0.7025 (t70) cc_final: 0.6608 (t70) REVERT: E 106 PHE cc_start: 0.6508 (m-10) cc_final: 0.6271 (m-10) REVERT: E 205 SER cc_start: 0.7276 (p) cc_final: 0.6847 (m) REVERT: E 328 ARG cc_start: 0.7162 (mmm160) cc_final: 0.6737 (mmm160) REVERT: E 645 THR cc_start: 0.9073 (p) cc_final: 0.8564 (t) REVERT: E 737 ASP cc_start: 0.8020 (p0) cc_final: 0.7640 (p0) REVERT: E 775 ASP cc_start: 0.8744 (p0) cc_final: 0.8453 (p0) REVERT: E 873 TYR cc_start: 0.8501 (m-80) cc_final: 0.8299 (m-80) REVERT: E 898 PHE cc_start: 0.8597 (t80) cc_final: 0.8360 (t80) REVERT: E 918 GLU cc_start: 0.8891 (tt0) cc_final: 0.8404 (tm-30) REVERT: E 950 ASP cc_start: 0.8402 (m-30) cc_final: 0.7918 (m-30) REVERT: E 962 LEU cc_start: 0.9321 (tp) cc_final: 0.9090 (tp) REVERT: E 1007 TYR cc_start: 0.7947 (t80) cc_final: 0.7189 (t80) REVERT: E 1010 GLN cc_start: 0.8146 (tp40) cc_final: 0.7773 (tp-100) REVERT: E 1050 MET cc_start: 0.7632 (ppp) cc_final: 0.7076 (ppp) REVERT: I 98 TYR cc_start: 0.8605 (t80) cc_final: 0.8188 (t80) REVERT: K 81 MET cc_start: 0.3878 (tpt) cc_final: 0.3538 (tpt) REVERT: L 4 MET cc_start: 0.4951 (mtp) cc_final: 0.2149 (mpp) REVERT: L 42 TYR cc_start: 0.5105 (m-80) cc_final: 0.4839 (m-80) REVERT: L 109 LYS cc_start: 0.6823 (tttt) cc_final: 0.6339 (tptt) outliers start: 3 outliers final: 0 residues processed: 530 average time/residue: 0.2076 time to fit residues: 183.9576 Evaluate side-chains 424 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 1.388 ------------------------------------------------------------------------------- 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: 7.9990 chunk 306 optimal weight: 1.9990 chunk 207 optimal weight: 10.0000 chunk 327 optimal weight: 0.4980 chunk 236 optimal weight: 20.0000 chunk 233 optimal weight: 0.9990 chunk 13 optimal weight: 0.3980 chunk 108 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 chunk 375 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 506 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** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** 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 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.172237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.138402 restraints weight = 119249.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.141781 restraints weight = 76840.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.144086 restraints weight = 55000.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.145625 restraints weight = 42926.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.146948 restraints weight = 35861.210| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.2667 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= 0.138 Angle : 0.761 18.828 49849 Z= 0.373 Chirality : 0.050 0.363 5919 Planarity : 0.005 0.103 6211 Dihedral : 5.859 32.352 4749 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.03 % Favored : 89.88 % Rotamer: Outliers : 0.08 % Allowed : 0.65 % Favored : 99.27 % 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: -2.95 (0.12), residues: 4377 helix: -1.01 (0.19), residues: 670 sheet: -1.70 (0.21), residues: 590 loop : -2.40 (0.11), residues: 3117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 995 TYR 0.035 0.002 TYR A 873 PHE 0.025 0.002 PHE H 29 TRP 0.041 0.002 TRP C 152 HIS 0.015 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (36349) covalent geometry : angle 0.72901 / 0.37 (49459) SS BOND : bond 0.00324 / 0.22 ( 48) SS BOND : angle 1.33192 / 0.84 ( 96) hydrogen bonds : bond 0.04608 / 3.10 ( 735) hydrogen bonds : angle 6.96778 / 4.82 ( 1944) Misc. bond : bond 0.00056 / 0.04 ( 2) link_ALPHA1-3 : bond 0.01057 / 0.60 ( 5) link_ALPHA1-3 : angle 2.33533 / 1.60 ( 15) link_ALPHA1-6 : bond 0.00435 / 0.24 ( 8) link_ALPHA1-6 : angle 1.56221 / 0.97 ( 24) link_BETA1-2 : bond 0.00796 / 0.53 ( 1) link_BETA1-2 : angle 1.21697 / 0.90 ( 3) link_BETA1-4 : bond 0.00784 / 0.56 ( 36) link_BETA1-4 : angle 2.22160 / 1.36 ( 108) link_BETA1-6 : bond 0.00642 / 0.38 ( 5) link_BETA1-6 : angle 1.11704 / 0.69 ( 15) link_NAG-ASN : bond 0.00641 / 0.41 ( 43) link_NAG-ASN : angle 3.65686 / 2.61 ( 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 535 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 532 time to evaluate : 1.369 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 92 PHE cc_start: 0.6741 (t80) cc_final: 0.6482 (t80) REVERT: A 220 PHE cc_start: 0.7980 (p90) cc_final: 0.7763 (p90) REVERT: A 298 GLU cc_start: 0.8599 (tp30) cc_final: 0.8297 (tp30) REVERT: A 314 GLN cc_start: 0.7809 (tm-30) cc_final: 0.7299 (tm-30) REVERT: A 406 GLU cc_start: 0.6201 (mt-10) cc_final: 0.5914 (mt-10) REVERT: A 773 GLU cc_start: 0.7377 (tm-30) cc_final: 0.7120 (tm-30) REVERT: A 774 GLN cc_start: 0.8412 (mp10) cc_final: 0.8091 (mp10) REVERT: A 777 ASN cc_start: 0.8598 (m110) cc_final: 0.8340 (m110) REVERT: A 882 ILE cc_start: 0.9458 (mt) cc_final: 0.9235 (mt) REVERT: A 905 ARG cc_start: 0.7283 (ptp-110) cc_final: 0.6995 (ptp-170) REVERT: A 1028 LYS cc_start: 0.9378 (mtpt) cc_final: 0.8864 (tptp) REVERT: A 1033 VAL cc_start: 0.8551 (t) cc_final: 0.7961 (t) REVERT: A 1052 PHE cc_start: 0.8965 (m-10) cc_final: 0.8644 (m-10) REVERT: C 80 ASP cc_start: 0.8387 (t0) cc_final: 0.7982 (t0) REVERT: C 354 ASN cc_start: 0.9458 (t0) cc_final: 0.9169 (t0) REVERT: C 396 TYR cc_start: 0.8461 (m-80) cc_final: 0.8084 (m-80) REVERT: C 742 ILE cc_start: 0.8885 (mm) cc_final: 0.8401 (mm) REVERT: C 765 ARG cc_start: 0.8504 (mtp-110) cc_final: 0.8237 (ptm-80) REVERT: C 777 ASN cc_start: 0.8845 (m110) cc_final: 0.8617 (m110) REVERT: C 790 LYS cc_start: 0.8023 (mmpt) cc_final: 0.7629 (mmmt) REVERT: C 900 MET cc_start: 0.3620 (mpp) cc_final: 0.2556 (mpp) REVERT: C 902 MET cc_start: 0.8170 (pmm) cc_final: 0.7087 (pmm) REVERT: C 1004 LEU cc_start: 0.9233 (mt) cc_final: 0.8892 (mt) REVERT: C 1018 ILE cc_start: 0.9361 (mt) cc_final: 0.8420 (mt) REVERT: C 1050 MET cc_start: 0.6975 (ttt) cc_final: 0.6526 (ttp) REVERT: C 1052 PHE cc_start: 0.8381 (m-10) cc_final: 0.7027 (m-10) REVERT: C 1103 PHE cc_start: 0.7913 (m-80) cc_final: 0.7581 (m-80) REVERT: C 1105 THR cc_start: 0.7216 (t) cc_final: 0.6398 (m) REVERT: C 1114 ILE cc_start: 0.7798 (mm) cc_final: 0.7475 (tp) REVERT: E 53 ASP cc_start: 0.6967 (t70) cc_final: 0.6550 (t70) REVERT: E 86 PHE cc_start: 0.5684 (t80) cc_final: 0.4488 (t80) REVERT: E 205 SER cc_start: 0.7206 (p) cc_final: 0.6683 (m) REVERT: E 328 ARG cc_start: 0.6992 (mmm160) cc_final: 0.6548 (mmm160) REVERT: E 645 THR cc_start: 0.9057 (p) cc_final: 0.8534 (t) REVERT: E 675 GLN cc_start: 0.8820 (tp-100) cc_final: 0.8097 (tp40) REVERT: E 677 GLN cc_start: 0.6700 (tm-30) cc_final: 0.6482 (tm-30) REVERT: E 737 ASP cc_start: 0.7979 (p0) cc_final: 0.7564 (p0) REVERT: E 775 ASP cc_start: 0.8677 (p0) cc_final: 0.8475 (p0) REVERT: E 873 TYR cc_start: 0.8483 (m-80) cc_final: 0.8246 (m-80) REVERT: E 950 ASP cc_start: 0.8285 (m-30) cc_final: 0.7754 (m-30) REVERT: E 962 LEU cc_start: 0.9308 (tp) cc_final: 0.9046 (tp) REVERT: E 1007 TYR cc_start: 0.7821 (t80) cc_final: 0.7108 (t80) REVERT: E 1010 GLN cc_start: 0.8048 (tp40) cc_final: 0.7654 (tp-100) REVERT: E 1050 MET cc_start: 0.7668 (ppp) cc_final: 0.7362 (ppp) REVERT: I 98 TYR cc_start: 0.8455 (t80) cc_final: 0.7973 (t80) REVERT: K 81 MET cc_start: 0.3767 (tpt) cc_final: 0.3398 (tpt) REVERT: L 4 MET cc_start: 0.4763 (mtp) cc_final: 0.1752 (mpp) REVERT: L 109 LYS cc_start: 0.6741 (tttt) cc_final: 0.6336 (tptt) outliers start: 3 outliers final: 0 residues processed: 535 average time/residue: 0.2109 time to fit residues: 188.7444 Evaluate side-chains 426 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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: 5.9990 chunk 167 optimal weight: 2.9990 chunk 397 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 317 optimal weight: 0.7980 chunk 281 optimal weight: 0.9990 chunk 247 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 395 optimal weight: 0.9990 chunk 306 optimal weight: 9.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** 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 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1036 GLN ** 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 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 928 ASN E 955 ASN ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN H 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 = 0.4498 r_free = 0.4498 target = 0.172706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.140351 restraints weight = 119538.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.143561 restraints weight = 80452.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.146280 restraints weight = 59083.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.147426 restraints weight = 43407.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.147902 restraints weight = 35602.995| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 36497 Z= 0.140 Angle : 0.782 18.842 49849 Z= 0.381 Chirality : 0.051 0.507 5919 Planarity : 0.006 0.122 6211 Dihedral : 5.810 31.842 4749 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.01 % Favored : 89.90 % Rotamer: Outliers : 0.10 % Allowed : 0.34 % Favored : 99.56 % 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: -2.94 (0.12), residues: 4377 helix: -1.09 (0.19), residues: 676 sheet: -1.74 (0.20), residues: 612 loop : -2.37 (0.11), residues: 3089 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 0.023 0.002 PHE E 275 TRP 0.029 0.002 TRP C 152 HIS 0.013 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (36349) covalent geometry : angle 0.73626 / 0.37 (49459) SS BOND : bond 0.00327 / 0.22 ( 48) SS BOND : angle 1.35727 / 0.84 ( 96) hydrogen bonds : bond 0.04648 / 3.12 ( 735) hydrogen bonds : angle 6.95232 / 4.79 ( 1944) Misc. bond : bond 0.00053 / 0.04 ( 2) link_ALPHA1-3 : bond 0.01058 / 0.60 ( 5) link_ALPHA1-3 : angle 2.29000 / 1.57 ( 15) link_ALPHA1-6 : bond 0.00448 / 0.26 ( 8) link_ALPHA1-6 : angle 1.55299 / 0.97 ( 24) link_BETA1-2 : bond 0.00784 / 0.52 ( 1) link_BETA1-2 : angle 1.19138 / 0.88 ( 3) link_BETA1-4 : bond 0.00883 / 0.61 ( 36) link_BETA1-4 : angle 2.20166 / 1.36 ( 108) link_BETA1-6 : bond 0.00641 / 0.39 ( 5) link_BETA1-6 : angle 1.12278 / 0.70 ( 15) link_NAG-ASN : bond 0.00645 / 0.41 ( 43) link_NAG-ASN : angle 4.66618 / 3.48 ( 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 521 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 517 time to evaluate : 1.308 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: A 92 PHE cc_start: 0.6712 (t80) cc_final: 0.6419 (t80) REVERT: A 190 ARG cc_start: 0.7576 (mmp-170) cc_final: 0.7286 (mmp-170) REVERT: A 220 PHE cc_start: 0.8000 (p90) cc_final: 0.7782 (p90) REVERT: A 298 GLU cc_start: 0.8567 (tp30) cc_final: 0.8257 (tp30) REVERT: A 314 GLN cc_start: 0.7754 (tm-30) cc_final: 0.7268 (tm-30) REVERT: A 734 THR cc_start: 0.9003 (p) cc_final: 0.8782 (p) REVERT: A 773 GLU cc_start: 0.7413 (tm-30) cc_final: 0.7127 (tm-30) REVERT: A 774 GLN cc_start: 0.8322 (mp10) cc_final: 0.8107 (mp10) REVERT: A 777 ASN cc_start: 0.8514 (m110) cc_final: 0.8197 (m110) REVERT: A 882 ILE cc_start: 0.9446 (mt) cc_final: 0.9242 (mt) REVERT: A 905 ARG cc_start: 0.7243 (ptp-110) cc_final: 0.6801 (ptp-170) REVERT: A 953 ASN cc_start: 0.8508 (m110) cc_final: 0.8255 (m110) REVERT: A 957 GLN cc_start: 0.8943 (mp10) cc_final: 0.8672 (pm20) REVERT: A 1028 LYS cc_start: 0.9342 (mtpt) cc_final: 0.8901 (tptp) REVERT: A 1033 VAL cc_start: 0.8522 (t) cc_final: 0.7641 (t) REVERT: A 1050 MET cc_start: 0.6622 (mpp) cc_final: 0.6408 (mmt) REVERT: A 1052 PHE cc_start: 0.8922 (m-10) cc_final: 0.8506 (m-10) REVERT: A 1062 PHE cc_start: 0.7835 (m-10) cc_final: 0.7119 (m-10) REVERT: A 1109 PHE cc_start: 0.8801 (t80) cc_final: 0.8393 (t80) REVERT: C 80 ASP cc_start: 0.8287 (t0) cc_final: 0.7927 (t0) REVERT: C 354 ASN cc_start: 0.9442 (t0) cc_final: 0.9147 (t0) REVERT: C 396 TYR cc_start: 0.8514 (m-80) cc_final: 0.8111 (m-80) REVERT: C 742 ILE cc_start: 0.8801 (mm) cc_final: 0.8553 (mm) REVERT: C 765 ARG cc_start: 0.8557 (mtp-110) cc_final: 0.8324 (ptm160) REVERT: C 777 ASN cc_start: 0.8768 (m110) cc_final: 0.8556 (m110) REVERT: C 790 LYS cc_start: 0.7970 (mmpt) cc_final: 0.7595 (mmmt) REVERT: C 900 MET cc_start: 0.3503 (mpp) cc_final: 0.2500 (mpp) REVERT: C 902 MET cc_start: 0.8170 (pmm) cc_final: 0.7186 (pmm) REVERT: C 1014 ARG cc_start: 0.8972 (mmt-90) cc_final: 0.8602 (mmt-90) REVERT: C 1018 ILE cc_start: 0.9265 (mt) cc_final: 0.8823 (mt) REVERT: C 1050 MET cc_start: 0.7071 (ttt) cc_final: 0.6609 (ttp) REVERT: C 1052 PHE cc_start: 0.8299 (m-10) cc_final: 0.6808 (m-10) REVERT: C 1103 PHE cc_start: 0.8182 (m-80) cc_final: 0.7964 (m-80) REVERT: C 1105 THR cc_start: 0.7143 (t) cc_final: 0.6479 (m) REVERT: E 53 ASP cc_start: 0.6859 (t70) cc_final: 0.6493 (t70) REVERT: E 86 PHE cc_start: 0.5314 (t80) cc_final: 0.4345 (t80) REVERT: E 205 SER cc_start: 0.7125 (p) cc_final: 0.6661 (m) REVERT: E 305 SER cc_start: 0.8320 (m) cc_final: 0.7830 (t) REVERT: E 645 THR cc_start: 0.8994 (p) cc_final: 0.8478 (t) REVERT: E 675 GLN cc_start: 0.8718 (tp-100) cc_final: 0.7978 (tp40) REVERT: E 737 ASP cc_start: 0.7961 (p0) cc_final: 0.7494 (p0) REVERT: E 776 LYS cc_start: 0.9121 (tttp) cc_final: 0.8608 (tptt) REVERT: E 873 TYR cc_start: 0.8366 (m-80) cc_final: 0.8134 (m-80) REVERT: E 925 ASN cc_start: 0.8947 (m110) cc_final: 0.8488 (m-40) REVERT: E 950 ASP cc_start: 0.8314 (m-30) cc_final: 0.7818 (m-30) REVERT: E 962 LEU cc_start: 0.9338 (tp) cc_final: 0.9093 (tp) REVERT: E 1007 TYR cc_start: 0.7808 (t80) cc_final: 0.7052 (t80) REVERT: E 1010 GLN cc_start: 0.8143 (tp40) cc_final: 0.7744 (tp-100) REVERT: E 1050 MET cc_start: 0.7679 (ppp) cc_final: 0.7459 (ppp) REVERT: I 98 TYR cc_start: 0.8393 (t80) cc_final: 0.7880 (t80) REVERT: L 4 MET cc_start: 0.4106 (mtp) cc_final: 0.1637 (mpp) REVERT: L 64 VAL cc_start: 0.5016 (t) cc_final: 0.4811 (p) REVERT: L 109 LYS cc_start: 0.6787 (tttt) cc_final: 0.6367 (tptt) outliers start: 4 outliers final: 0 residues processed: 521 average time/residue: 0.2062 time to fit residues: 178.7446 Evaluate side-chains 432 residues out of total 3863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 432 time to evaluate : 1.113 ------------------------------------------------------------------------------- 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: 10.0000 chunk 279 optimal weight: 0.9980 chunk 314 optimal weight: 0.0040 chunk 113 optimal weight: 9.9990 chunk 241 optimal weight: 4.9990 chunk 329 optimal weight: 30.0000 chunk 115 optimal weight: 0.9980 chunk 222 optimal weight: 5.9990 chunk 384 optimal weight: 0.0870 chunk 112 optimal weight: 10.0000 chunk 368 optimal weight: 20.0000 overall best weight: 1.4172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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** ** E 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 762 GLN ** E 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 955 ASN ** E 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN L 95 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.171806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.138703 restraints weight = 124385.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.141034 restraints weight = 84465.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.144252 restraints weight = 66153.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.145037 restraints weight = 46855.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.145180 restraints weight = 39391.795| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 36497 Z= 0.141 Angle : 0.770 18.855 49849 Z= 0.377 Chirality : 0.051 0.456 5919 Planarity : 0.006 0.103 6211 Dihedral : 5.771 31.315 4749 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.08 % Favored : 89.83 % Rotamer: Outliers : 0.08 % Allowed : 0.50 % Favored : 99.43 % 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: -2.90 (0.12), residues: 4377 helix: -1.02 (0.19), residues: 675 sheet: -1.61 (0.21), residues: 604 loop : -2.37 (0.11), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 995 TYR 0.035 0.002 TYR A 873 PHE 0.023 0.002 PHE E 201 TRP 0.034 0.002 TRP L 41 HIS 0.012 0.001 HIS E1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (36349) covalent geometry : angle 0.72994 / 0.37 (49459) SS BOND : bond 0.00381 / 0.24 ( 48) SS BOND : angle 1.33662 / 0.83 ( 96) hydrogen bonds : bond 0.04639 / 3.11 ( 735) hydrogen bonds : angle 6.95050 / 4.79 ( 1944) Misc. bond : bond 0.00057 / 0.04 ( 2) link_ALPHA1-3 : bond 0.01024 / 0.58 ( 5) link_ALPHA1-3 : angle 2.27761 / 1.56 ( 15) link_ALPHA1-6 : bond 0.00417 / 0.23 ( 8) link_ALPHA1-6 : angle 1.57036 / 0.97 ( 24) link_BETA1-2 : bond 0.00751 / 0.50 ( 1) link_BETA1-2 : angle 1.18026 / 0.88 ( 3) link_BETA1-4 : bond 0.00753 / 0.54 ( 36) link_BETA1-4 : angle 2.17770 / 1.33 ( 108) link_BETA1-6 : bond 0.00639 / 0.39 ( 5) link_BETA1-6 : angle 1.13527 / 0.70 ( 15) link_NAG-ASN : bond 0.00638 / 0.40 ( 43) link_NAG-ASN : angle 4.31017 / 3.22 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6551.75 seconds wall clock time: 114 minutes 48.49 seconds (6888.49 seconds total)