Starting phenix.real_space_refine on Mon May 19 17:09:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g40_29712/05_2025/8g40_29712.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g40_29712/05_2025/8g40_29712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g40_29712/05_2025/8g40_29712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g40_29712/05_2025/8g40_29712.map" model { file = "/net/cci-nas-00/data/ceres_data/8g40_29712/05_2025/8g40_29712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g40_29712/05_2025/8g40_29712.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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: 5 Type Number sf(0) Gaussians Ca 5 9.91 5 S 109 5.16 5 C 11569 2.51 5 N 3120 2.21 5 O 3847 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 130 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 18650 Number of models: 1 Model: "" Number of chains: 38 Chain: "G" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "A" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "B" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "M" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "I" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "C" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 989 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "N" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 101} Chain: "J" Number of atoms: 3001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3001 Classifications: {'peptide': 388} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 10, 'TRANS': 374} Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "k" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "s" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "3" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "e" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "l" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "t" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "2" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "4" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "5" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.09, per 1000 atoms: 0.65 Number of scatterers: 18650 At special positions: 0 Unit cell: (117.03, 142.76, 169.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 5 19.99 S 109 16.00 O 3847 8.00 N 3120 7.00 C 11569 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.06 Simple disulfide: pdb=" SG CYS G 124 " - pdb=" SG CYS G 129 " distance=2.07 Simple disulfide: pdb=" SG CYS G 175 " - pdb=" SG CYS G 193 " distance=2.04 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.08 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.07 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.07 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.09 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.08 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.14 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.05 Simple disulfide: pdb=" SG CYS H 124 " - pdb=" SG CYS H 129 " distance=2.07 Simple disulfide: pdb=" SG CYS H 175 " - pdb=" SG CYS H 193 " distance=2.03 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.10 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.08 Simple disulfide: pdb=" SG CYS H 278 " - pdb=" SG CYS H 291 " distance=2.07 Simple disulfide: pdb=" SG CYS H 280 " - pdb=" SG CYS H 289 " distance=2.09 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.09 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.15 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 92 " - pdb=" SG CYS I 417 " distance=2.03 Simple disulfide: pdb=" SG CYS I 124 " - pdb=" SG CYS I 129 " distance=2.11 Simple disulfide: pdb=" SG CYS I 175 " - pdb=" SG CYS I 193 " distance=2.05 Simple disulfide: pdb=" SG CYS I 183 " - pdb=" SG CYS I 230 " distance=2.08 Simple disulfide: pdb=" SG CYS I 232 " - pdb=" SG CYS I 237 " distance=2.06 Simple disulfide: pdb=" SG CYS I 278 " - pdb=" SG CYS I 291 " distance=2.08 Simple disulfide: pdb=" SG CYS I 280 " - pdb=" SG CYS I 289 " distance=2.09 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.09 Simple disulfide: pdb=" SG CYS I 421 " - pdb=" SG CYS I 447 " distance=2.16 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.05 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.07 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.02 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.07 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.03 Simple disulfide: pdb=" SG CYS J 183 " - pdb=" SG CYS J 230 " distance=2.09 Simple disulfide: pdb=" SG CYS J 232 " - pdb=" SG CYS J 237 " distance=2.06 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.08 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.09 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.08 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.13 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN 3 4 " - " MAN 3 5 " " MAN c 4 " - " MAN c 5 " " MAN k 4 " - " MAN k 5 " " MAN s 4 " - " MAN s 5 " ALPHA1-3 " BMA 3 3 " - " MAN 3 4 " " MAN 3 6 " - " MAN 3 7 " " BMA c 3 " - " MAN c 4 " " MAN c 6 " - " MAN c 7 " " BMA k 3 " - " MAN k 4 " " MAN k 6 " - " MAN k 7 " " BMA s 3 " - " MAN s 4 " " MAN s 6 " - " MAN s 7 " ALPHA1-6 " BMA 3 3 " - " MAN 3 6 " " MAN 3 6 " - " MAN 3 8 " " BMA c 3 " - " MAN c 6 " " MAN c 6 " - " MAN c 8 " " BMA j 3 " - " MAN j 4 " " BMA k 3 " - " MAN k 6 " " MAN k 6 " - " MAN k 8 " " BMA s 3 " - " MAN s 6 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 1 2 " - " BMA 1 3 " " NAG 2 1 " - " NAG 2 2 " " NAG 2 2 " - " BMA 2 3 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 4 2 " - " BMA 4 3 " " NAG 5 1 " - " NAG 5 2 " " NAG 7 1 " - " NAG 7 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " " NAG q 2 " - " BMA q 3 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG t 2 " - " BMA t 3 " " NAG u 1 " - " NAG u 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG 4 1 " - " FUC 4 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG 5 1 " - " FUC 5 3 " " NAG d 1 " - " FUC d 4 " " NAG e 1 " - " FUC e 3 " " NAG l 1 " - " FUC l 4 " " NAG m 1 " - " FUC m 3 " " NAG t 1 " - " FUC t 4 " " NAG u 1 " - " FUC u 3 " NAG-ASN " NAG 1 1 " - " ASN J 86 " " NAG 2 1 " - " ASN J 146 " " NAG 3 1 " - " ASN J 200 " " NAG 4 1 " - " ASN J 234 " " NAG 5 1 " - " ASN J 245 " " NAG 7 1 " - " ASN J 367 " " NAG a 1 " - " ASN G 86 " " NAG b 1 " - " ASN G 146 " " NAG c 1 " - " ASN G 200 " " NAG d 1 " - " ASN G 234 " " NAG e 1 " - " ASN G 245 " " NAG g 1 " - " ASN G 367 " " NAG i 1 " - " ASN H 86 " " NAG j 1 " - " ASN H 146 " " NAG k 1 " - " ASN H 200 " " NAG l 1 " - " ASN H 234 " " NAG m 1 " - " ASN H 245 " " NAG o 1 " - " ASN H 367 " " NAG q 1 " - " ASN I 86 " " NAG r 1 " - " ASN I 146 " " NAG s 1 " - " ASN I 200 " " NAG t 1 " - " ASN I 234 " " NAG u 1 " - " ASN I 245 " " NAG w 1 " - " ASN I 367 " Time building additional restraints: 6.31 Conformation dependent library (CDL) restraints added in 2.3 seconds 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4096 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 41 sheets defined 5.0% alpha, 41.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.696A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 251 Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.711A pdb=" N LYS A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.955A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.729A pdb=" N ASN H 146 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 251 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.687A pdb=" N LYS B 31 " --> pdb=" O GLY B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.985A pdb=" N PHE M 83 " --> pdb=" O SER M 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 110 Processing helix chain 'I' and resid 247 through 251 Processing helix chain 'C' and resid 27 through 32 removed outlier: 3.704A pdb=" N LYS C 31 " --> pdb=" O GLY C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.877A pdb=" N PHE N 83 " --> pdb=" O SER N 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 110 Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.733A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 96 through 102 removed outlier: 5.422A pdb=" N PHE G 97 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR G 449 " --> pdb=" O PHE G 97 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N CYS G 447 " --> pdb=" O PRO G 99 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.818A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.154A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 231 through 233 removed outlier: 3.503A pdb=" N VAL G 231 " --> pdb=" O THR G 238 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.406A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 352 through 356 removed outlier: 4.591A pdb=" N TRP G 352 " --> pdb=" O GLY G 363 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY G 363 " --> pdb=" O TRP G 352 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ASP G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.420A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.538A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.517A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.631A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.269A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.333A pdb=" N LEU A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 10 through 12 removed outlier: 4.281A pdb=" N PHE A 117 " --> pdb=" O THR A 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.763A pdb=" N GLN L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.415A pdb=" N LEU L 33 " --> pdb=" O PHE L 49 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 96 through 102 removed outlier: 5.385A pdb=" N PHE H 97 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N THR H 449 " --> pdb=" O PHE H 97 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N CYS H 447 " --> pdb=" O PRO H 99 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.809A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.166A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.518A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.406A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 352 through 356 removed outlier: 4.548A pdb=" N TRP H 352 " --> pdb=" O GLY H 363 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY H 363 " --> pdb=" O TRP H 352 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.453A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.522A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.472A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.564A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.280A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AC1, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.313A pdb=" N LEU B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY B 50 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 10 through 12 removed outlier: 4.311A pdb=" N PHE B 117 " --> pdb=" O THR B 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AC4, first strand: chain 'M' and resid 4 through 7 removed outlier: 3.895A pdb=" N GLN M 70 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER M 67 " --> pdb=" O GLN M 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.381A pdb=" N LEU M 33 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N PHE M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 96 through 102 removed outlier: 5.403A pdb=" N PHE I 97 " --> pdb=" O THR I 449 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR I 449 " --> pdb=" O PHE I 97 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N CYS I 447 " --> pdb=" O PRO I 99 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ARG I 420 " --> pdb=" O GLY I 448 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 115 through 124 removed outlier: 4.818A pdb=" N TRP I 115 " --> pdb=" O THR I 138 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR I 138 " --> pdb=" O TRP I 115 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N THR I 117 " --> pdb=" O GLN I 136 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN I 136 " --> pdb=" O THR I 117 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N GLU I 119 " --> pdb=" O LEU I 134 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU I 134 " --> pdb=" O GLU I 119 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR I 157 " --> pdb=" O GLY I 135 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU I 158 " --> pdb=" O VAL I 174 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS I 172 " --> pdb=" O MET I 160 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 179 through 184 removed outlier: 4.108A pdb=" N ASP I 197 " --> pdb=" O ASN I 200 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR I 207 " --> pdb=" O LEU I 211 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LEU I 211 " --> pdb=" O TYR I 207 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 231 through 233 removed outlier: 6.537A pdb=" N GLU I 258 " --> pdb=" O ILE I 262 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE I 262 " --> pdb=" O GLU I 258 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 276 through 283 removed outlier: 5.425A pdb=" N GLU I 277 " --> pdb=" O ARG I 292 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ARG I 292 " --> pdb=" O GLU I 277 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 352 through 356 removed outlier: 4.649A pdb=" N TRP I 352 " --> pdb=" O GLY I 363 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY I 363 " --> pdb=" O TRP I 352 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ASP I 402 " --> pdb=" O GLY I 373 " (cutoff:3.500A) removed outlier: 9.638A pdb=" N GLU I 375 " --> pdb=" O ARG I 400 " (cutoff:3.500A) removed outlier: 10.472A pdb=" N ARG I 400 " --> pdb=" O GLU I 375 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N PHE I 377 " --> pdb=" O VAL I 398 " (cutoff:3.500A) removed outlier: 13.494A pdb=" N VAL I 398 " --> pdb=" O PHE I 377 " (cutoff:3.500A) removed outlier: 15.354A pdb=" N VAL I 379 " --> pdb=" O VAL I 396 " (cutoff:3.500A) removed outlier: 16.233A pdb=" N VAL I 396 " --> pdb=" O VAL I 379 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AD4, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.332A pdb=" N LEU C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLY C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 10 through 12 removed outlier: 4.307A pdb=" N PHE C 117 " --> pdb=" O THR C 98 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AD7, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.685A pdb=" N GLN N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.407A pdb=" N LEU N 33 " --> pdb=" O PHE N 49 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 96 through 102 removed outlier: 5.437A pdb=" N PHE J 97 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR J 449 " --> pdb=" O PHE J 97 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N CYS J 447 " --> pdb=" O PRO J 99 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.779A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.284A pdb=" N ASP J 197 " --> pdb=" O ASN J 200 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR J 207 " --> pdb=" O LEU J 211 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 231 through 233 removed outlier: 3.500A pdb=" N VAL J 231 " --> pdb=" O THR J 238 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.396A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 352 through 356 removed outlier: 4.623A pdb=" N TRP J 352 " --> pdb=" O GLY J 363 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY J 363 " --> pdb=" O TRP J 352 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASP J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.500A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.507A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.839A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.338A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1542 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: 6.60 Time building geometry restraints manager: 7.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2965 1.30 - 1.44: 5354 1.44 - 1.57: 10597 1.57 - 1.71: 0 1.71 - 1.84: 134 Bond restraints: 19050 Sorted by residual: bond pdb=" C SER G 88 " pdb=" O SER G 88 " ideal model delta sigma weight residual 1.235 1.302 -0.067 1.26e-02 6.30e+03 2.79e+01 bond pdb=" C PRO I 166 " pdb=" O PRO I 166 " ideal model delta sigma weight residual 1.232 1.170 0.062 1.27e-02 6.20e+03 2.40e+01 bond pdb=" C LYS J 249 " pdb=" O LYS J 249 " ideal model delta sigma weight residual 1.233 1.284 -0.050 1.06e-02 8.90e+03 2.24e+01 bond pdb=" N GLY J 286 " pdb=" CA GLY J 286 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.99e+01 bond pdb=" C GLY G 93 " pdb=" O GLY G 93 " ideal model delta sigma weight residual 1.235 1.175 0.060 1.35e-02 5.49e+03 1.99e+01 ... (remaining 19045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 21953 2.34 - 4.67: 3622 4.67 - 7.01: 280 7.01 - 9.35: 9 9.35 - 11.69: 1 Bond angle restraints: 25865 Sorted by residual: angle pdb=" N LYS J 128 " pdb=" CA LYS J 128 " pdb=" CB LYS J 128 " ideal model delta sigma weight residual 111.52 99.83 11.69 1.86e+00 2.89e-01 3.95e+01 angle pdb=" CA ASP G 125 " pdb=" CB ASP G 125 " pdb=" CG ASP G 125 " ideal model delta sigma weight residual 112.60 117.90 -5.30 1.00e+00 1.00e+00 2.81e+01 angle pdb=" N ILE H 397 " pdb=" CA ILE H 397 " pdb=" C ILE H 397 " ideal model delta sigma weight residual 111.81 107.35 4.46 8.60e-01 1.35e+00 2.69e+01 angle pdb=" N ILE I 397 " pdb=" CA ILE I 397 " pdb=" C ILE I 397 " ideal model delta sigma weight residual 111.81 107.37 4.44 8.60e-01 1.35e+00 2.67e+01 angle pdb=" CA ASP J 243 " pdb=" CB ASP J 243 " pdb=" CG ASP J 243 " ideal model delta sigma weight residual 112.60 117.74 -5.14 1.00e+00 1.00e+00 2.64e+01 ... (remaining 25860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 11670 22.36 - 44.72: 496 44.72 - 67.07: 88 67.07 - 89.43: 105 89.43 - 111.79: 65 Dihedral angle restraints: 12424 sinusoidal: 5991 harmonic: 6433 Sorted by residual: dihedral pdb=" CA GLY G 297 " pdb=" C GLY G 297 " pdb=" N SER G 298 " pdb=" CA SER G 298 " ideal model delta harmonic sigma weight residual 180.00 147.27 32.73 0 5.00e+00 4.00e-02 4.29e+01 dihedral pdb=" CA ALA C 40 " pdb=" C ALA C 40 " pdb=" N PRO C 41 " pdb=" CA PRO C 41 " ideal model delta harmonic sigma weight residual -180.00 -147.75 -32.25 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA GLY J 297 " pdb=" C GLY J 297 " pdb=" N SER J 298 " pdb=" CA SER J 298 " ideal model delta harmonic sigma weight residual 180.00 148.23 31.77 0 5.00e+00 4.00e-02 4.04e+01 ... (remaining 12421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1860 0.083 - 0.165: 1028 0.165 - 0.248: 200 0.248 - 0.331: 8 0.331 - 0.414: 3 Chirality restraints: 3099 Sorted by residual: chirality pdb=" C1 MAN k 4 " pdb=" O3 BMA k 3 " pdb=" C2 MAN k 4 " pdb=" O5 MAN k 4 " both_signs ideal model delta sigma weight residual False 2.40 2.21 0.19 2.00e-02 2.50e+03 8.56e+01 chirality pdb=" C1 MAN 3 4 " pdb=" O3 BMA 3 3 " pdb=" C2 MAN 3 4 " pdb=" O5 MAN 3 4 " both_signs ideal model delta sigma weight residual False 2.40 2.22 0.18 2.00e-02 2.50e+03 8.38e+01 chirality pdb=" C1 MAN s 4 " pdb=" O3 BMA s 3 " pdb=" C2 MAN s 4 " pdb=" O5 MAN s 4 " both_signs ideal model delta sigma weight residual False 2.40 2.25 0.15 2.00e-02 2.50e+03 5.26e+01 ... (remaining 3096 not shown) Planarity restraints: 3213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG 3 1 " 0.129 2.00e-02 2.50e+03 1.07e-01 1.43e+02 pdb=" C7 NAG 3 1 " -0.059 2.00e-02 2.50e+03 pdb=" C8 NAG 3 1 " 0.105 2.00e-02 2.50e+03 pdb=" N2 NAG 3 1 " -0.161 2.00e-02 2.50e+03 pdb=" O7 NAG 3 1 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG m 2 " 0.104 2.00e-02 2.50e+03 8.57e-02 9.18e+01 pdb=" C7 NAG m 2 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG m 2 " 0.081 2.00e-02 2.50e+03 pdb=" N2 NAG m 2 " -0.134 2.00e-02 2.50e+03 pdb=" O7 NAG m 2 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG s 1 " -0.087 2.00e-02 2.50e+03 7.36e-02 6.77e+01 pdb=" C7 NAG s 1 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG s 1 " -0.077 2.00e-02 2.50e+03 pdb=" N2 NAG s 1 " 0.102 2.00e-02 2.50e+03 pdb=" O7 NAG s 1 " 0.006 2.00e-02 2.50e+03 ... (remaining 3210 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1034 2.74 - 3.28: 18576 3.28 - 3.82: 31170 3.82 - 4.36: 43610 4.36 - 4.90: 69557 Nonbonded interactions: 163947 Sorted by model distance: nonbonded pdb=" O HIS I 347 " pdb="CA CA I2000 " model vdw 2.196 2.510 nonbonded pdb=" OD2 ASP J 324 " pdb="CA CA J2000 " model vdw 2.230 2.510 nonbonded pdb=" O HIS H 347 " pdb="CA CA H2000 " model vdw 2.242 2.510 nonbonded pdb=" O HIS J 347 " pdb="CA CA J2000 " model vdw 2.272 2.510 nonbonded pdb=" OD2 ASP G 324 " pdb="CA CA G 501 " model vdw 2.291 2.510 ... (remaining 163942 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 '1' and resid 1 through 2) selection = (chain '2' and resid 1 through 2) selection = (chain '5' and resid 1 through 2) selection = (chain 'a' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) selection = (chain 'q' and resid 1 through 2) selection = (chain 'r' and resid 1 through 2) selection = (chain 'u' and resid 1 through 2) } ncs_group { reference = (chain '3' and (resid 2 or resid 5 through 8)) selection = (chain 'c' and (resid 2 or resid 5 through 8)) selection = (chain 'k' and (resid 2 or resid 5 through 8)) selection = (chain 's' and (resid 1 or resid 4 through 7)) } ncs_group { reference = (chain '4' and resid 1 through 3) selection = (chain 'd' and resid 1 through 3) selection = (chain 'j' and resid 1 through 3) selection = (chain 'l' and resid 1 through 3) selection = (chain 't' and resid 1 through 3) } ncs_group { reference = chain '7' selection = chain 'g' selection = chain 'o' selection = chain 'w' } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'G' and (resid 82 through 469 or resid 501)) selection = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 46.020 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 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 : 0.015 0.130 19184 Z= 1.003 Angle : 1.719 15.558 26225 Z= 1.070 Chirality : 0.093 0.414 3099 Planarity : 0.011 0.107 3189 Dihedral : 17.440 111.790 8202 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 0.58 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.37 % Favored : 95.32 % Rotamer: Outliers : 0.42 % Allowed : 3.01 % Favored : 96.57 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 1.23 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.17), residues: 2243 helix: -1.44 (0.89), residues: 24 sheet: 0.23 (0.17), residues: 893 loop : -1.01 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.014 TRP G 115 HIS 0.040 0.008 HIS J 336 PHE 0.073 0.012 PHE I 205 TYR 0.076 0.014 TYR I 281 ARG 0.028 0.004 ARG H 210 Details of bonding type rmsd link_NAG-ASN : bond 0.01252 ( 24) link_NAG-ASN : angle 5.50225 ( 72) link_ALPHA1-6 : bond 0.01180 ( 8) link_ALPHA1-6 : angle 2.85536 ( 24) link_BETA1-4 : bond 0.01344 ( 40) link_BETA1-4 : angle 4.51537 ( 120) link_ALPHA1-2 : bond 0.00626 ( 4) link_ALPHA1-2 : angle 4.91729 ( 12) link_ALPHA1-3 : bond 0.01824 ( 8) link_ALPHA1-3 : angle 2.93549 ( 24) hydrogen bonds : bond 0.15068 ( 573) hydrogen bonds : angle 8.49223 ( 1542) link_BETA1-6 : bond 0.01264 ( 8) link_BETA1-6 : angle 4.69590 ( 24) SS BOND : bond 0.05337 ( 42) SS BOND : angle 2.58498 ( 84) covalent geometry : bond 0.01466 (19050) covalent geometry : angle 1.65812 (25865) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 261 time to evaluate : 1.985 Fit side-chains REVERT: G 400 ARG cc_start: 0.8857 (ptm-80) cc_final: 0.8517 (ptm-80) REVERT: L 75 ILE cc_start: 0.9297 (mt) cc_final: 0.8991 (mt) REVERT: L 101 GLN cc_start: 0.9163 (mm110) cc_final: 0.8800 (pm20) REVERT: H 356 ASP cc_start: 0.8842 (t0) cc_final: 0.8520 (t0) REVERT: H 400 ARG cc_start: 0.8699 (ptm-80) cc_final: 0.8127 (ptp90) REVERT: B 62 GLN cc_start: 0.8814 (mp10) cc_final: 0.8548 (mp10) REVERT: B 63 LYS cc_start: 0.9152 (ptmt) cc_final: 0.8947 (ptpp) REVERT: B 65 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8027 (mt0) REVERT: M 69 THR cc_start: 0.9249 (p) cc_final: 0.8991 (p) REVERT: M 74 THR cc_start: 0.9097 (m) cc_final: 0.8820 (t) REVERT: M 80 SER cc_start: 0.8998 (m) cc_final: 0.8744 (p) REVERT: M 82 ASP cc_start: 0.8971 (m-30) cc_final: 0.8736 (m-30) REVERT: I 465 ASN cc_start: 0.8976 (m-40) cc_final: 0.8542 (t0) REVERT: J 83 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8366 (tt0) REVERT: J 249 LYS cc_start: 0.8673 (ttpt) cc_final: 0.8077 (tmmt) REVERT: J 400 ARG cc_start: 0.8960 (ptm-80) cc_final: 0.8594 (ptm160) outliers start: 8 outliers final: 5 residues processed: 267 average time/residue: 1.2500 time to fit residues: 376.8369 Evaluate side-chains 218 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 213 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 178 TRP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain H residue 178 TRP Chi-restraints excluded: chain I residue 178 TRP Chi-restraints excluded: chain J residue 178 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 184 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 170 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 ASN B 6 GLN M 32 ASN M 79 GLN M 92 ASN I 274 HIS I 468 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.095652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.072300 restraints weight = 31581.925| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.52 r_work: 0.2754 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19184 Z= 0.151 Angle : 0.754 8.645 26225 Z= 0.375 Chirality : 0.049 0.268 3099 Planarity : 0.004 0.037 3189 Dihedral : 13.372 80.423 4297 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.90 % Favored : 96.92 % Rotamer: Outliers : 1.35 % Allowed : 8.25 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2243 helix: -0.50 (0.89), residues: 24 sheet: 0.22 (0.17), residues: 890 loop : -0.29 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 115 HIS 0.011 0.001 HIS I 336 PHE 0.018 0.002 PHE N 83 TYR 0.019 0.002 TYR L 91 ARG 0.008 0.001 ARG M 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 24) link_NAG-ASN : angle 3.11233 ( 72) link_ALPHA1-6 : bond 0.00783 ( 8) link_ALPHA1-6 : angle 1.41429 ( 24) link_BETA1-4 : bond 0.00492 ( 40) link_BETA1-4 : angle 2.71623 ( 120) link_ALPHA1-2 : bond 0.00423 ( 4) link_ALPHA1-2 : angle 2.11322 ( 12) link_ALPHA1-3 : bond 0.00997 ( 8) link_ALPHA1-3 : angle 2.11290 ( 24) hydrogen bonds : bond 0.04586 ( 573) hydrogen bonds : angle 7.10666 ( 1542) link_BETA1-6 : bond 0.00515 ( 8) link_BETA1-6 : angle 2.02654 ( 24) SS BOND : bond 0.00337 ( 42) SS BOND : angle 1.13797 ( 84) covalent geometry : bond 0.00326 (19050) covalent geometry : angle 0.70683 (25865) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 233 time to evaluate : 2.025 Fit side-chains revert: symmetry clash REVERT: G 230 CYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8598 (p) REVERT: G 400 ARG cc_start: 0.8511 (ptm-80) cc_final: 0.7970 (ptm-80) REVERT: L 75 ILE cc_start: 0.9047 (mt) cc_final: 0.8699 (mt) REVERT: L 101 GLN cc_start: 0.8805 (mm110) cc_final: 0.8498 (pm20) REVERT: H 199 LYS cc_start: 0.8911 (tttt) cc_final: 0.8546 (ttpt) REVERT: H 400 ARG cc_start: 0.8463 (ptm-80) cc_final: 0.7672 (ptp90) REVERT: B 62 GLN cc_start: 0.8089 (mp10) cc_final: 0.7827 (mp10) REVERT: B 63 LYS cc_start: 0.8975 (ptmt) cc_final: 0.8610 (ptpp) REVERT: B 65 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8268 (tp40) REVERT: B 76 THR cc_start: 0.9085 (p) cc_final: 0.8872 (t) REVERT: B 123 LEU cc_start: 0.8891 (tp) cc_final: 0.8614 (tm) REVERT: M 18 ARG cc_start: 0.8712 (mtp-110) cc_final: 0.8103 (ttt180) REVERT: M 20 THR cc_start: 0.8783 (p) cc_final: 0.8349 (t) REVERT: M 21 LEU cc_start: 0.9086 (mt) cc_final: 0.8885 (mm) REVERT: M 69 THR cc_start: 0.8952 (p) cc_final: 0.8697 (p) REVERT: M 74 THR cc_start: 0.8912 (m) cc_final: 0.8677 (t) REVERT: M 82 ASP cc_start: 0.8850 (m-30) cc_final: 0.8333 (m-30) REVERT: M 107 ILE cc_start: 0.6884 (OUTLIER) cc_final: 0.6622 (pp) REVERT: I 141 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8500 (t0) REVERT: I 465 ASN cc_start: 0.8597 (m-40) cc_final: 0.8229 (t0) REVERT: C 62 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8044 (tp-100) REVERT: J 83 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7810 (tt0) REVERT: J 249 LYS cc_start: 0.8024 (ttpt) cc_final: 0.7401 (tmmt) REVERT: J 400 ARG cc_start: 0.8770 (ptm-80) cc_final: 0.8211 (ptm160) outliers start: 26 outliers final: 10 residues processed: 242 average time/residue: 1.3748 time to fit residues: 375.6397 Evaluate side-chains 216 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 202 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 15 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 chunk 205 optimal weight: 0.0170 chunk 166 optimal weight: 9.9990 overall best weight: 2.8026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 347 HIS A 3 GLN H 141 ASN B 6 GLN M 42 GLN I 347 HIS ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 468 HIS C 120 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.093029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.069825 restraints weight = 32020.742| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.53 r_work: 0.2710 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 19184 Z= 0.305 Angle : 0.795 15.937 26225 Z= 0.388 Chirality : 0.052 0.252 3099 Planarity : 0.004 0.044 3189 Dihedral : 10.959 74.256 4289 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 2.49 % Allowed : 9.34 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2243 helix: -0.01 (0.94), residues: 24 sheet: 0.08 (0.17), residues: 895 loop : -0.32 (0.17), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 115 HIS 0.006 0.002 HIS I 168 PHE 0.017 0.002 PHE G 410 TYR 0.026 0.002 TYR G 121 ARG 0.006 0.001 ARG J 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00432 ( 24) link_NAG-ASN : angle 3.06669 ( 72) link_ALPHA1-6 : bond 0.00423 ( 8) link_ALPHA1-6 : angle 1.56477 ( 24) link_BETA1-4 : bond 0.00434 ( 40) link_BETA1-4 : angle 2.80089 ( 120) link_ALPHA1-2 : bond 0.00181 ( 4) link_ALPHA1-2 : angle 2.48263 ( 12) link_ALPHA1-3 : bond 0.00445 ( 8) link_ALPHA1-3 : angle 2.46505 ( 24) hydrogen bonds : bond 0.04716 ( 573) hydrogen bonds : angle 6.86565 ( 1542) link_BETA1-6 : bond 0.00551 ( 8) link_BETA1-6 : angle 1.90634 ( 24) SS BOND : bond 0.00548 ( 42) SS BOND : angle 1.33669 ( 84) covalent geometry : bond 0.00706 (19050) covalent geometry : angle 0.74744 (25865) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 208 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8585 (ptm-80) cc_final: 0.8322 (ptm160) REVERT: A 65 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8341 (mt0) REVERT: L 27 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7638 (mtp85) REVERT: L 101 GLN cc_start: 0.8884 (mm110) cc_final: 0.8534 (pm20) REVERT: H 199 LYS cc_start: 0.8948 (tttt) cc_final: 0.8600 (ttpt) REVERT: H 230 CYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8684 (p) REVERT: H 400 ARG cc_start: 0.8511 (ptm-80) cc_final: 0.7677 (ptp90) REVERT: B 62 GLN cc_start: 0.8220 (mp10) cc_final: 0.7891 (mp10) REVERT: B 63 LYS cc_start: 0.9006 (ptmt) cc_final: 0.8719 (ptpp) REVERT: B 65 GLN cc_start: 0.8547 (mm-40) cc_final: 0.8331 (tp40) REVERT: B 123 LEU cc_start: 0.8928 (tp) cc_final: 0.8640 (tm) REVERT: M 42 GLN cc_start: 0.8768 (mt0) cc_final: 0.8501 (mt0) REVERT: M 61 ARG cc_start: 0.8590 (ptt90) cc_final: 0.8186 (ptt-90) REVERT: M 74 THR cc_start: 0.8964 (m) cc_final: 0.8692 (t) REVERT: M 82 ASP cc_start: 0.8782 (m-30) cc_final: 0.8210 (m-30) REVERT: M 107 ILE cc_start: 0.6855 (OUTLIER) cc_final: 0.6554 (pp) REVERT: I 465 ASN cc_start: 0.8627 (m-40) cc_final: 0.8262 (t0) REVERT: C 13 ARG cc_start: 0.8752 (mmm-85) cc_final: 0.8502 (mmm160) REVERT: C 62 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.8023 (tp-100) REVERT: J 141 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8451 (t0) REVERT: J 249 LYS cc_start: 0.8036 (ttpt) cc_final: 0.7371 (tmmt) REVERT: J 400 ARG cc_start: 0.8818 (ptm-80) cc_final: 0.8279 (ptm160) outliers start: 48 outliers final: 22 residues processed: 229 average time/residue: 1.2885 time to fit residues: 332.0885 Evaluate side-chains 216 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain J residue 141 ASN Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 465 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 93 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 HIS B 6 GLN ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 468 HIS C 120 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.095038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.071911 restraints weight = 31838.626| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.53 r_work: 0.2751 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19184 Z= 0.167 Angle : 0.680 9.803 26225 Z= 0.333 Chirality : 0.048 0.269 3099 Planarity : 0.003 0.044 3189 Dihedral : 8.712 64.771 4289 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.99 % Favored : 96.83 % Rotamer: Outliers : 1.92 % Allowed : 10.85 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2243 helix: -1.03 (0.81), residues: 28 sheet: 0.13 (0.17), residues: 903 loop : -0.38 (0.17), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 178 HIS 0.003 0.001 HIS J 336 PHE 0.015 0.002 PHE H 410 TYR 0.015 0.002 TYR G 121 ARG 0.008 0.000 ARG M 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00280 ( 24) link_NAG-ASN : angle 2.62892 ( 72) link_ALPHA1-6 : bond 0.00541 ( 8) link_ALPHA1-6 : angle 1.38456 ( 24) link_BETA1-4 : bond 0.00427 ( 40) link_BETA1-4 : angle 2.42323 ( 120) link_ALPHA1-2 : bond 0.00323 ( 4) link_ALPHA1-2 : angle 2.30222 ( 12) link_ALPHA1-3 : bond 0.00768 ( 8) link_ALPHA1-3 : angle 1.91632 ( 24) hydrogen bonds : bond 0.03913 ( 573) hydrogen bonds : angle 6.49367 ( 1542) link_BETA1-6 : bond 0.00511 ( 8) link_BETA1-6 : angle 1.77873 ( 24) SS BOND : bond 0.00314 ( 42) SS BOND : angle 0.88204 ( 84) covalent geometry : bond 0.00371 (19050) covalent geometry : angle 0.63971 (25865) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8524 (ptm-80) cc_final: 0.8293 (ptm160) REVERT: G 432 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8537 (mp0) REVERT: A 13 ARG cc_start: 0.8801 (mmm-85) cc_final: 0.8497 (mmm-85) REVERT: L 27 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7595 (mtp85) REVERT: L 101 GLN cc_start: 0.8859 (mm110) cc_final: 0.8481 (pm20) REVERT: H 199 LYS cc_start: 0.8893 (tttt) cc_final: 0.8448 (mtmt) REVERT: H 400 ARG cc_start: 0.8454 (ptm-80) cc_final: 0.7619 (ptp90) REVERT: B 62 GLN cc_start: 0.8121 (mp10) cc_final: 0.7828 (mp10) REVERT: B 63 LYS cc_start: 0.8967 (ptmt) cc_final: 0.8697 (ptpp) REVERT: B 65 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8176 (tp40) REVERT: B 123 LEU cc_start: 0.8954 (tp) cc_final: 0.8667 (tm) REVERT: M 18 ARG cc_start: 0.8469 (mtp-110) cc_final: 0.7777 (ttm170) REVERT: M 42 GLN cc_start: 0.8719 (mt0) cc_final: 0.8450 (mt0) REVERT: M 61 ARG cc_start: 0.8677 (ptt90) cc_final: 0.8244 (ptt-90) REVERT: M 74 THR cc_start: 0.8963 (m) cc_final: 0.8685 (t) REVERT: M 82 ASP cc_start: 0.8780 (m-30) cc_final: 0.8451 (m-30) REVERT: M 107 ILE cc_start: 0.6932 (OUTLIER) cc_final: 0.6642 (pp) REVERT: I 141 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8554 (t0) REVERT: I 465 ASN cc_start: 0.8583 (m-40) cc_final: 0.8294 (t0) REVERT: C 62 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8038 (tp-100) REVERT: C 87 ARG cc_start: 0.6614 (mpt180) cc_final: 0.6278 (mpt180) REVERT: J 249 LYS cc_start: 0.7985 (ttpt) cc_final: 0.7334 (tmmt) REVERT: J 400 ARG cc_start: 0.8808 (ptm-80) cc_final: 0.8295 (ptm160) outliers start: 37 outliers final: 17 residues processed: 219 average time/residue: 1.4108 time to fit residues: 345.7190 Evaluate side-chains 208 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 175 optimal weight: 6.9990 chunk 119 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 171 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 182 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN L 90 HIS B 6 GLN M 70 GLN ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 468 HIS C 120 GLN N 6 GLN N 79 GLN J 274 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.095692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.072782 restraints weight = 31878.714| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.53 r_work: 0.2771 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19184 Z= 0.144 Angle : 0.638 10.168 26225 Z= 0.313 Chirality : 0.046 0.241 3099 Planarity : 0.003 0.041 3189 Dihedral : 7.515 58.211 4289 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.25 % Favored : 96.57 % Rotamer: Outliers : 2.08 % Allowed : 11.73 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2243 helix: -1.07 (0.77), residues: 28 sheet: 0.19 (0.17), residues: 871 loop : -0.28 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 178 HIS 0.003 0.001 HIS I 274 PHE 0.014 0.002 PHE H 410 TYR 0.015 0.001 TYR G 121 ARG 0.009 0.000 ARG J 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 24) link_NAG-ASN : angle 2.46288 ( 72) link_ALPHA1-6 : bond 0.00564 ( 8) link_ALPHA1-6 : angle 1.38894 ( 24) link_BETA1-4 : bond 0.00431 ( 40) link_BETA1-4 : angle 2.11627 ( 120) link_ALPHA1-2 : bond 0.00294 ( 4) link_ALPHA1-2 : angle 2.21037 ( 12) link_ALPHA1-3 : bond 0.00803 ( 8) link_ALPHA1-3 : angle 1.88186 ( 24) hydrogen bonds : bond 0.03676 ( 573) hydrogen bonds : angle 6.26315 ( 1542) link_BETA1-6 : bond 0.00493 ( 8) link_BETA1-6 : angle 1.74302 ( 24) SS BOND : bond 0.00299 ( 42) SS BOND : angle 0.78815 ( 84) covalent geometry : bond 0.00319 (19050) covalent geometry : angle 0.60285 (25865) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8539 (ptm-80) cc_final: 0.8242 (ptm-80) REVERT: G 432 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8594 (mp0) REVERT: A 107 ASP cc_start: 0.8796 (t0) cc_final: 0.8551 (t0) REVERT: L 27 ARG cc_start: 0.8243 (ttp80) cc_final: 0.7637 (mtp85) REVERT: L 61 ARG cc_start: 0.9008 (ptp90) cc_final: 0.8654 (ptp90) REVERT: L 101 GLN cc_start: 0.8879 (mm110) cc_final: 0.8496 (pm20) REVERT: H 199 LYS cc_start: 0.8850 (tttt) cc_final: 0.8443 (mtmt) REVERT: H 400 ARG cc_start: 0.8414 (ptm-80) cc_final: 0.7593 (ptp90) REVERT: B 3 GLN cc_start: 0.8465 (mm110) cc_final: 0.8002 (mm110) REVERT: B 62 GLN cc_start: 0.8098 (mp10) cc_final: 0.7801 (mp10) REVERT: B 63 LYS cc_start: 0.8965 (ptmt) cc_final: 0.8672 (ptpp) REVERT: B 65 GLN cc_start: 0.8361 (mm-40) cc_final: 0.8016 (tp40) REVERT: B 123 LEU cc_start: 0.8976 (tp) cc_final: 0.8688 (tm) REVERT: M 18 ARG cc_start: 0.8461 (mtp-110) cc_final: 0.7902 (ttm170) REVERT: M 61 ARG cc_start: 0.8628 (ptt90) cc_final: 0.8210 (ptt-90) REVERT: M 74 THR cc_start: 0.8960 (m) cc_final: 0.8646 (t) REVERT: M 82 ASP cc_start: 0.8818 (m-30) cc_final: 0.8439 (m-30) REVERT: M 107 ILE cc_start: 0.6856 (OUTLIER) cc_final: 0.6614 (pp) REVERT: I 465 ASN cc_start: 0.8599 (m-40) cc_final: 0.8254 (t0) REVERT: C 23 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8909 (tptt) REVERT: C 90 ASP cc_start: 0.8240 (m-30) cc_final: 0.8016 (m-30) REVERT: N 54 ARG cc_start: 0.8512 (mtp85) cc_final: 0.8278 (mtp85) REVERT: N 81 GLU cc_start: 0.8862 (pt0) cc_final: 0.8655 (pt0) REVERT: J 249 LYS cc_start: 0.7974 (ttpt) cc_final: 0.7329 (tmmt) REVERT: J 400 ARG cc_start: 0.8781 (ptm-80) cc_final: 0.8266 (ptm160) outliers start: 40 outliers final: 21 residues processed: 225 average time/residue: 1.3653 time to fit residues: 348.9454 Evaluate side-chains 220 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 2.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 362 MET Chi-restraints excluded: chain H residue 390 LEU Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 3 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 145 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 274 HIS ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN L 90 HIS B 6 GLN M 70 GLN ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.093782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.070658 restraints weight = 32204.568| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.56 r_work: 0.2726 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 19184 Z= 0.261 Angle : 0.702 10.219 26225 Z= 0.347 Chirality : 0.048 0.218 3099 Planarity : 0.004 0.043 3189 Dihedral : 7.881 64.318 4288 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.66 % Favored : 96.17 % Rotamer: Outliers : 2.34 % Allowed : 11.73 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2243 helix: -0.92 (0.82), residues: 28 sheet: 0.00 (0.17), residues: 906 loop : -0.38 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 178 HIS 0.004 0.001 HIS G 191 PHE 0.016 0.002 PHE G 410 TYR 0.022 0.002 TYR G 121 ARG 0.009 0.001 ARG J 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 24) link_NAG-ASN : angle 2.68565 ( 72) link_ALPHA1-6 : bond 0.00369 ( 8) link_ALPHA1-6 : angle 1.51803 ( 24) link_BETA1-4 : bond 0.00353 ( 40) link_BETA1-4 : angle 2.03192 ( 120) link_ALPHA1-2 : bond 0.00094 ( 4) link_ALPHA1-2 : angle 2.35991 ( 12) link_ALPHA1-3 : bond 0.00443 ( 8) link_ALPHA1-3 : angle 2.36121 ( 24) hydrogen bonds : bond 0.04185 ( 573) hydrogen bonds : angle 6.45244 ( 1542) link_BETA1-6 : bond 0.00522 ( 8) link_BETA1-6 : angle 1.77875 ( 24) SS BOND : bond 0.00416 ( 42) SS BOND : angle 0.97924 ( 84) covalent geometry : bond 0.00603 (19050) covalent geometry : angle 0.66648 (25865) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8611 (ptm-80) cc_final: 0.8308 (ptm-80) REVERT: G 432 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8635 (mp0) REVERT: A 13 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8452 (mmm-85) REVERT: A 23 LYS cc_start: 0.8757 (tttm) cc_final: 0.8523 (ttpt) REVERT: L 27 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7628 (mtp85) REVERT: L 101 GLN cc_start: 0.8902 (mm110) cc_final: 0.8506 (pm20) REVERT: H 199 LYS cc_start: 0.8873 (tttt) cc_final: 0.8434 (mtmt) REVERT: H 400 ARG cc_start: 0.8410 (ptm-80) cc_final: 0.7547 (ptp90) REVERT: B 62 GLN cc_start: 0.8208 (mp10) cc_final: 0.7825 (mp10) REVERT: B 63 LYS cc_start: 0.9015 (ptmt) cc_final: 0.8765 (ptpp) REVERT: B 65 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8155 (tp40) REVERT: B 123 LEU cc_start: 0.8943 (tp) cc_final: 0.8643 (tm) REVERT: M 18 ARG cc_start: 0.8404 (mtp-110) cc_final: 0.7848 (ttm170) REVERT: M 61 ARG cc_start: 0.8593 (ptt90) cc_final: 0.8080 (ptt-90) REVERT: M 74 THR cc_start: 0.8942 (m) cc_final: 0.8643 (t) REVERT: M 82 ASP cc_start: 0.8866 (m-30) cc_final: 0.8555 (m-30) REVERT: M 107 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6683 (pp) REVERT: I 199 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8516 (mttt) REVERT: I 465 ASN cc_start: 0.8631 (m-40) cc_final: 0.8292 (t0) REVERT: C 23 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8834 (tptt) REVERT: N 31 ASP cc_start: 0.8928 (p0) cc_final: 0.8700 (p0) REVERT: J 249 LYS cc_start: 0.8050 (ttpt) cc_final: 0.7366 (tmmt) REVERT: J 400 ARG cc_start: 0.8795 (ptm-80) cc_final: 0.8270 (ptm160) outliers start: 45 outliers final: 29 residues processed: 220 average time/residue: 1.3378 time to fit residues: 331.0034 Evaluate side-chains 221 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 90 HIS Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 362 MET Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 69 THR Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 465 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 195 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 38 optimal weight: 0.0980 chunk 175 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 197 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 206 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN L 90 HIS B 6 GLN M 70 GLN ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 468 HIS ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.096428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.073580 restraints weight = 31387.219| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 2.53 r_work: 0.2787 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19184 Z= 0.115 Angle : 0.618 11.000 26225 Z= 0.306 Chirality : 0.045 0.236 3099 Planarity : 0.003 0.041 3189 Dihedral : 7.127 54.789 4288 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.03 % Favored : 96.79 % Rotamer: Outliers : 1.71 % Allowed : 13.03 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2243 helix: -1.20 (0.75), residues: 28 sheet: 0.13 (0.17), residues: 874 loop : -0.23 (0.17), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP I 178 HIS 0.017 0.001 HIS L 90 PHE 0.014 0.001 PHE H 410 TYR 0.012 0.001 TYR L 91 ARG 0.010 0.000 ARG J 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00230 ( 24) link_NAG-ASN : angle 2.31469 ( 72) link_ALPHA1-6 : bond 0.00593 ( 8) link_ALPHA1-6 : angle 1.35700 ( 24) link_BETA1-4 : bond 0.00440 ( 40) link_BETA1-4 : angle 1.71969 ( 120) link_ALPHA1-2 : bond 0.00344 ( 4) link_ALPHA1-2 : angle 2.29180 ( 12) link_ALPHA1-3 : bond 0.00891 ( 8) link_ALPHA1-3 : angle 1.70905 ( 24) hydrogen bonds : bond 0.03492 ( 573) hydrogen bonds : angle 6.16429 ( 1542) link_BETA1-6 : bond 0.00489 ( 8) link_BETA1-6 : angle 1.64825 ( 24) SS BOND : bond 0.00234 ( 42) SS BOND : angle 0.87426 ( 84) covalent geometry : bond 0.00246 (19050) covalent geometry : angle 0.58875 (25865) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 2.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8526 (ptm-80) cc_final: 0.8268 (ptm160) REVERT: G 432 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8621 (mp0) REVERT: A 23 LYS cc_start: 0.8793 (tttm) cc_final: 0.8511 (ttpt) REVERT: A 65 GLN cc_start: 0.8032 (mt0) cc_final: 0.7820 (tt0) REVERT: A 107 ASP cc_start: 0.8778 (t0) cc_final: 0.8558 (t0) REVERT: L 27 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7458 (mtp85) REVERT: L 61 ARG cc_start: 0.8991 (ptp90) cc_final: 0.8696 (ptp90) REVERT: L 101 GLN cc_start: 0.8859 (mm110) cc_final: 0.8491 (pm20) REVERT: H 199 LYS cc_start: 0.8795 (tttt) cc_final: 0.8381 (mtmt) REVERT: H 261 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8350 (tmtt) REVERT: H 400 ARG cc_start: 0.8326 (ptm-80) cc_final: 0.7507 (ptp90) REVERT: B 3 GLN cc_start: 0.8494 (mm110) cc_final: 0.8032 (mm110) REVERT: B 23 LYS cc_start: 0.8795 (mmmt) cc_final: 0.8284 (mmtm) REVERT: B 62 GLN cc_start: 0.8127 (mp10) cc_final: 0.7719 (mp10) REVERT: B 63 LYS cc_start: 0.8977 (ptmt) cc_final: 0.8679 (ptpp) REVERT: B 123 LEU cc_start: 0.8954 (tp) cc_final: 0.8659 (tm) REVERT: M 18 ARG cc_start: 0.8388 (mtp-110) cc_final: 0.7876 (ttm170) REVERT: M 61 ARG cc_start: 0.8590 (ptt90) cc_final: 0.8191 (ptt-90) REVERT: M 74 THR cc_start: 0.8960 (m) cc_final: 0.8657 (t) REVERT: M 82 ASP cc_start: 0.8854 (m-30) cc_final: 0.8237 (m-30) REVERT: I 465 ASN cc_start: 0.8605 (m-40) cc_final: 0.8280 (t0) REVERT: C 23 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8891 (tptt) REVERT: C 90 ASP cc_start: 0.8330 (m-30) cc_final: 0.8066 (m-30) REVERT: N 54 ARG cc_start: 0.8517 (mtp85) cc_final: 0.8294 (mtp85) REVERT: J 249 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7307 (tmmt) REVERT: J 400 ARG cc_start: 0.8754 (ptm-80) cc_final: 0.8239 (ptm160) outliers start: 33 outliers final: 17 residues processed: 223 average time/residue: 1.3532 time to fit residues: 338.2306 Evaluate side-chains 214 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 195 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain H residue 362 MET Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 104 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 179 optimal weight: 0.9980 chunk 134 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN B 6 GLN ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.095045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.072104 restraints weight = 31945.228| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.54 r_work: 0.2758 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19184 Z= 0.190 Angle : 0.649 11.186 26225 Z= 0.321 Chirality : 0.046 0.225 3099 Planarity : 0.004 0.050 3189 Dihedral : 7.220 57.041 4288 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.21 % Rotamer: Outliers : 1.97 % Allowed : 13.39 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2243 helix: -1.00 (0.78), residues: 28 sheet: 0.07 (0.17), residues: 898 loop : -0.27 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 178 HIS 0.003 0.001 HIS I 274 PHE 0.015 0.002 PHE H 410 TYR 0.018 0.002 TYR C 32 ARG 0.012 0.000 ARG J 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 24) link_NAG-ASN : angle 2.42854 ( 72) link_ALPHA1-6 : bond 0.00482 ( 8) link_ALPHA1-6 : angle 1.44743 ( 24) link_BETA1-4 : bond 0.00374 ( 40) link_BETA1-4 : angle 1.75144 ( 120) link_ALPHA1-2 : bond 0.00156 ( 4) link_ALPHA1-2 : angle 2.23690 ( 12) link_ALPHA1-3 : bond 0.00609 ( 8) link_ALPHA1-3 : angle 2.06581 ( 24) hydrogen bonds : bond 0.03780 ( 573) hydrogen bonds : angle 6.24019 ( 1542) link_BETA1-6 : bond 0.00489 ( 8) link_BETA1-6 : angle 1.64831 ( 24) SS BOND : bond 0.00405 ( 42) SS BOND : angle 0.90329 ( 84) covalent geometry : bond 0.00436 (19050) covalent geometry : angle 0.61863 (25865) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 1.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8551 (ptm-80) cc_final: 0.8290 (ptm160) REVERT: G 432 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8641 (mp0) REVERT: G 467 MET cc_start: 0.8935 (ptm) cc_final: 0.8545 (ptm) REVERT: A 23 LYS cc_start: 0.8794 (tttm) cc_final: 0.8520 (ttpt) REVERT: L 61 ARG cc_start: 0.9010 (ptp90) cc_final: 0.8699 (ptp90) REVERT: L 101 GLN cc_start: 0.8847 (mm110) cc_final: 0.8493 (pm20) REVERT: H 199 LYS cc_start: 0.8816 (tttt) cc_final: 0.8426 (mtmt) REVERT: H 261 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8382 (tmtt) REVERT: H 400 ARG cc_start: 0.8363 (ptm-80) cc_final: 0.7512 (ptp90) REVERT: B 3 GLN cc_start: 0.8490 (mm110) cc_final: 0.8026 (mm110) REVERT: B 62 GLN cc_start: 0.8196 (mp10) cc_final: 0.7815 (mp10) REVERT: B 63 LYS cc_start: 0.8984 (ptmt) cc_final: 0.8660 (ptpp) REVERT: B 65 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8186 (tp40) REVERT: B 123 LEU cc_start: 0.8955 (tp) cc_final: 0.8653 (tm) REVERT: M 61 ARG cc_start: 0.8562 (ptt90) cc_final: 0.8127 (ptt-90) REVERT: M 74 THR cc_start: 0.8959 (m) cc_final: 0.8722 (t) REVERT: M 82 ASP cc_start: 0.8895 (m-30) cc_final: 0.8279 (m-30) REVERT: I 465 ASN cc_start: 0.8628 (m-40) cc_final: 0.8285 (t0) REVERT: C 23 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8886 (tptt) REVERT: C 90 ASP cc_start: 0.8293 (m-30) cc_final: 0.8037 (m-30) REVERT: N 54 ARG cc_start: 0.8552 (mtp85) cc_final: 0.8327 (mtp85) REVERT: J 227 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7460 (mp0) REVERT: J 249 LYS cc_start: 0.7970 (ttpt) cc_final: 0.7313 (tmmt) REVERT: J 400 ARG cc_start: 0.8764 (ptm-80) cc_final: 0.8255 (ptm160) outliers start: 38 outliers final: 22 residues processed: 220 average time/residue: 1.2789 time to fit residues: 317.1103 Evaluate side-chains 219 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain H residue 362 MET Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain J residue 227 GLU Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 465 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 204 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 196 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN B 6 GLN ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 468 HIS C 62 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 90 HIS N 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.072978 restraints weight = 31786.162| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.53 r_work: 0.2775 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19184 Z= 0.153 Angle : 0.640 11.264 26225 Z= 0.317 Chirality : 0.046 0.235 3099 Planarity : 0.004 0.052 3189 Dihedral : 7.007 53.990 4288 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.39 % Favored : 96.43 % Rotamer: Outliers : 1.50 % Allowed : 14.22 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2243 helix: -1.03 (0.77), residues: 28 sheet: 0.10 (0.17), residues: 896 loop : -0.30 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 178 HIS 0.008 0.001 HIS H 336 PHE 0.014 0.002 PHE H 410 TYR 0.015 0.001 TYR G 121 ARG 0.013 0.000 ARG M 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 24) link_NAG-ASN : angle 2.30715 ( 72) link_ALPHA1-6 : bond 0.00523 ( 8) link_ALPHA1-6 : angle 1.40507 ( 24) link_BETA1-4 : bond 0.00400 ( 40) link_BETA1-4 : angle 1.63890 ( 120) link_ALPHA1-2 : bond 0.00233 ( 4) link_ALPHA1-2 : angle 2.25087 ( 12) link_ALPHA1-3 : bond 0.00763 ( 8) link_ALPHA1-3 : angle 1.88412 ( 24) hydrogen bonds : bond 0.03610 ( 573) hydrogen bonds : angle 6.15683 ( 1542) link_BETA1-6 : bond 0.00484 ( 8) link_BETA1-6 : angle 1.60022 ( 24) SS BOND : bond 0.00307 ( 42) SS BOND : angle 1.40382 ( 84) covalent geometry : bond 0.00343 (19050) covalent geometry : angle 0.60998 (25865) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 198 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.8289 (ptm160) REVERT: G 432 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8647 (mp0) REVERT: G 467 MET cc_start: 0.8920 (ptm) cc_final: 0.8504 (ptm) REVERT: A 23 LYS cc_start: 0.8775 (tttm) cc_final: 0.8501 (ttpt) REVERT: L 27 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7461 (mtp85) REVERT: L 61 ARG cc_start: 0.9005 (ptp90) cc_final: 0.8688 (ptp90) REVERT: L 101 GLN cc_start: 0.8839 (mm110) cc_final: 0.8505 (pm20) REVERT: H 199 LYS cc_start: 0.8808 (tttt) cc_final: 0.8390 (mtmt) REVERT: H 261 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8352 (tmtt) REVERT: H 400 ARG cc_start: 0.8371 (ptm-80) cc_final: 0.7525 (ptp90) REVERT: B 3 GLN cc_start: 0.8507 (mm110) cc_final: 0.8030 (mm110) REVERT: B 23 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8301 (mmtm) REVERT: B 62 GLN cc_start: 0.8176 (mp10) cc_final: 0.7827 (mp10) REVERT: B 63 LYS cc_start: 0.8974 (ptmt) cc_final: 0.8665 (ptpp) REVERT: B 65 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8132 (tp40) REVERT: B 123 LEU cc_start: 0.8948 (tp) cc_final: 0.8647 (tm) REVERT: M 18 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.7768 (ttm170) REVERT: M 61 ARG cc_start: 0.8561 (ptt90) cc_final: 0.8134 (ptt-90) REVERT: M 74 THR cc_start: 0.8945 (m) cc_final: 0.8669 (t) REVERT: M 82 ASP cc_start: 0.8887 (m-30) cc_final: 0.8254 (m-30) REVERT: I 85 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7900 (mtm180) REVERT: I 465 ASN cc_start: 0.8629 (m-40) cc_final: 0.8297 (t0) REVERT: C 23 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8880 (tptt) REVERT: C 90 ASP cc_start: 0.8264 (m-30) cc_final: 0.8053 (m-30) REVERT: N 54 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8310 (mtp85) REVERT: J 249 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7293 (tmmt) REVERT: J 400 ARG cc_start: 0.8759 (ptm-80) cc_final: 0.8254 (ptm160) outliers start: 29 outliers final: 21 residues processed: 216 average time/residue: 1.3240 time to fit residues: 321.3888 Evaluate side-chains 217 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 199 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 211 optimal weight: 2.9990 chunk 108 optimal weight: 0.0970 chunk 157 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN B 6 GLN ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.073016 restraints weight = 31716.325| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.54 r_work: 0.2775 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19184 Z= 0.156 Angle : 0.638 11.438 26225 Z= 0.316 Chirality : 0.046 0.223 3099 Planarity : 0.004 0.055 3189 Dihedral : 6.934 53.096 4288 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.48 % Favored : 96.34 % Rotamer: Outliers : 1.71 % Allowed : 14.17 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2243 helix: -1.03 (0.77), residues: 28 sheet: 0.10 (0.17), residues: 896 loop : -0.30 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 178 HIS 0.003 0.001 HIS I 274 PHE 0.014 0.002 PHE H 410 TYR 0.020 0.001 TYR C 32 ARG 0.013 0.000 ARG J 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 24) link_NAG-ASN : angle 2.29523 ( 72) link_ALPHA1-6 : bond 0.00530 ( 8) link_ALPHA1-6 : angle 1.41461 ( 24) link_BETA1-4 : bond 0.00396 ( 40) link_BETA1-4 : angle 1.61639 ( 120) link_ALPHA1-2 : bond 0.00220 ( 4) link_ALPHA1-2 : angle 2.21894 ( 12) link_ALPHA1-3 : bond 0.00723 ( 8) link_ALPHA1-3 : angle 1.88304 ( 24) hydrogen bonds : bond 0.03605 ( 573) hydrogen bonds : angle 6.14941 ( 1542) link_BETA1-6 : bond 0.00487 ( 8) link_BETA1-6 : angle 1.59008 ( 24) SS BOND : bond 0.00291 ( 42) SS BOND : angle 1.23070 ( 84) covalent geometry : bond 0.00352 (19050) covalent geometry : angle 0.60937 (25865) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4486 Ramachandran restraints generated. 2243 Oldfield, 0 Emsley, 2243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 195 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8569 (ptm-80) cc_final: 0.8292 (ptm160) REVERT: G 432 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8624 (mp0) REVERT: G 467 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8476 (ptm) REVERT: A 23 LYS cc_start: 0.8785 (tttm) cc_final: 0.8499 (ttpt) REVERT: A 26 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: L 27 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7434 (mtp85) REVERT: L 61 ARG cc_start: 0.9026 (ptp90) cc_final: 0.8699 (ptp90) REVERT: L 101 GLN cc_start: 0.8795 (mm110) cc_final: 0.8470 (pm20) REVERT: H 199 LYS cc_start: 0.8795 (tttt) cc_final: 0.8425 (mtmt) REVERT: H 261 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8355 (tmtt) REVERT: H 400 ARG cc_start: 0.8393 (ptm-80) cc_final: 0.7550 (ptp90) REVERT: B 3 GLN cc_start: 0.8517 (mm110) cc_final: 0.8045 (mm110) REVERT: B 23 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8305 (mmtm) REVERT: B 62 GLN cc_start: 0.8164 (mp10) cc_final: 0.7822 (mp10) REVERT: B 63 LYS cc_start: 0.8965 (ptmt) cc_final: 0.8655 (ptpp) REVERT: B 65 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8131 (tp40) REVERT: B 123 LEU cc_start: 0.8965 (tp) cc_final: 0.8667 (tm) REVERT: M 18 ARG cc_start: 0.8388 (mtp-110) cc_final: 0.7888 (ttm170) REVERT: M 61 ARG cc_start: 0.8539 (ptt90) cc_final: 0.8119 (ptt-90) REVERT: M 74 THR cc_start: 0.8941 (m) cc_final: 0.8708 (t) REVERT: M 82 ASP cc_start: 0.8893 (m-30) cc_final: 0.8264 (m-30) REVERT: I 85 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7918 (mtm180) REVERT: I 465 ASN cc_start: 0.8620 (m-40) cc_final: 0.8292 (t0) REVERT: C 23 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8881 (tptt) REVERT: N 54 ARG cc_start: 0.8546 (mtp85) cc_final: 0.8318 (mtp85) REVERT: J 249 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7298 (tmmt) REVERT: J 400 ARG cc_start: 0.8772 (ptm-80) cc_final: 0.8269 (ptm160) outliers start: 33 outliers final: 22 residues processed: 215 average time/residue: 1.3029 time to fit residues: 314.8816 Evaluate side-chains 220 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 467 MET Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain H residue 318 CYS Chi-restraints excluded: chain B residue 11 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 141 ASN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 90 optimal weight: 2.9990 chunk 214 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 204 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN H 141 ASN B 6 GLN ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.094625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.071661 restraints weight = 31943.165| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.52 r_work: 0.2748 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19184 Z= 0.236 Angle : 0.679 11.652 26225 Z= 0.337 Chirality : 0.047 0.226 3099 Planarity : 0.004 0.053 3189 Dihedral : 7.247 57.522 4288 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.21 % Rotamer: Outliers : 1.71 % Allowed : 14.27 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2243 helix: -0.90 (0.81), residues: 28 sheet: 0.06 (0.17), residues: 896 loop : -0.38 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 178 HIS 0.004 0.001 HIS G 191 PHE 0.016 0.002 PHE H 410 TYR 0.019 0.002 TYR G 121 ARG 0.013 0.001 ARG J 150 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 24) link_NAG-ASN : angle 2.45353 ( 72) link_ALPHA1-6 : bond 0.00401 ( 8) link_ALPHA1-6 : angle 1.48288 ( 24) link_BETA1-4 : bond 0.00353 ( 40) link_BETA1-4 : angle 1.68736 ( 120) link_ALPHA1-2 : bond 0.00077 ( 4) link_ALPHA1-2 : angle 2.27691 ( 12) link_ALPHA1-3 : bond 0.00513 ( 8) link_ALPHA1-3 : angle 2.20056 ( 24) hydrogen bonds : bond 0.03937 ( 573) hydrogen bonds : angle 6.29918 ( 1542) link_BETA1-6 : bond 0.00484 ( 8) link_BETA1-6 : angle 1.62734 ( 24) SS BOND : bond 0.00377 ( 42) SS BOND : angle 1.30279 ( 84) covalent geometry : bond 0.00542 (19050) covalent geometry : angle 0.64892 (25865) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12099.61 seconds wall clock time: 209 minutes 51.40 seconds (12591.40 seconds total)