Starting phenix.real_space_refine on Sat Jul 4 05:47:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8g40_29712/07_2026/8g40_29712.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g40_29712/07_2026/8g40_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8g40_29712/07_2026/8g40_29712.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8g40_29712/07_2026/8g40_29712.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g40_29712/07_2026/8g40_29712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g40_29712/07_2026/8g40_29712.map" model { file = "/net/cci-nas-00/data/ceres_data/8g40_29712/07_2026/8g40_29712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g40_29712/07_2026/8g40_29712.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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 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 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 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 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 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 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 chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 chiralities: 2 Chain: "q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "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 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 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 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 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 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 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 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 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 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: 4.13, per 1000 atoms: 0.22 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: 2.21 Conformation dependent library (CDL) restraints added in 693.3 milliseconds 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: 0.54 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: 3.29 Time building geometry restraints manager: 2.70 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 - 17.62: 9767 17.62 - 35.23: 642 35.23 - 52.85: 122 52.85 - 70.46: 45 70.46 - 88.08: 20 Dihedral angle restraints: 10596 sinusoidal: 4163 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 10593 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 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: 5.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.400 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9166 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 : 13.443 88.075 6374 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (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 ARG 0.028 0.004 ARG H 210 TYR 0.076 0.014 TYR I 281 PHE 0.073 0.012 PHE I 205 TRP 0.076 0.014 TRP G 115 HIS 0.040 0.008 HIS J 336 Details of bonding type rmsd/Z covalent geometry : bond 0.01466 / 1.00 (19050) covalent geometry : angle 1.65812 / 1.06 (25865) SS BOND : bond 0.05337 / 3.68 ( 42) SS BOND : angle 2.58498 / 1.80 ( 84) hydrogen bonds : bond 0.15068 / 9.53 ( 573) hydrogen bonds : angle 8.49223 / 5.97 ( 1542) link_ALPHA1-2 : bond 0.00626 / 0.28 ( 4) link_ALPHA1-2 : angle 4.91729 / 3.01 ( 12) link_ALPHA1-3 : bond 0.01824 / 1.10 ( 8) link_ALPHA1-3 : angle 2.93549 / 1.90 ( 24) link_ALPHA1-6 : bond 0.01180 / 0.60 ( 8) link_ALPHA1-6 : angle 2.85536 / 1.75 ( 24) link_BETA1-4 : bond 0.01344 / 0.81 ( 40) link_BETA1-4 : angle 4.51537 / 3.13 ( 120) link_BETA1-6 : bond 0.01264 / 0.77 ( 8) link_BETA1-6 : angle 4.69590 / 2.80 ( 24) link_NAG-ASN : bond 0.01252 / 0.74 ( 24) link_NAG-ASN : angle 5.50225 / 3.79 ( 72) *********************** 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 : 0.736 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 18 ARG cc_start: 0.8631 (ttt-90) cc_final: 0.8412 (mtp-110) REVERT: M 69 THR cc_start: 0.9249 (p) cc_final: 0.9034 (p) REVERT: M 74 THR cc_start: 0.9097 (m) cc_final: 0.8798 (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: 0.8661 (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: 0.5571 time to fit residues: 167.5791 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 : 0.600 ------------------------------------------------------------------------------- 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 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.0020 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 2.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 141 ASN B 6 GLN M 32 ASN M 92 ASN I 274 HIS I 468 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.096504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.073182 restraints weight = 31613.245| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.56 r_work: 0.2772 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2647 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19184 Z= 0.137 Angle : 0.711 8.583 26225 Z= 0.360 Chirality : 0.047 0.270 3099 Planarity : 0.004 0.028 3189 Dihedral : 6.267 26.837 2469 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.85 % Favored : 96.97 % Rotamer: Outliers : 1.30 % Allowed : 8.30 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2243 helix: -0.61 (0.90), residues: 24 sheet: 0.26 (0.17), residues: 890 loop : -0.26 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 87 TYR 0.017 0.002 TYR L 91 PHE 0.018 0.002 PHE N 83 TRP 0.016 0.002 TRP G 115 HIS 0.009 0.001 HIS I 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (19050) covalent geometry : angle 0.67477 / 0.35 (25865) SS BOND : bond 0.00343 / 0.21 ( 42) SS BOND : angle 1.09402 / 0.88 ( 84) hydrogen bonds : bond 0.04415 / 2.92 ( 573) hydrogen bonds : angle 7.05454 / 4.95 ( 1542) link_ALPHA1-2 : bond 0.00460 / 0.19 ( 4) link_ALPHA1-2 : angle 1.72630 / 0.88 ( 12) link_ALPHA1-3 : bond 0.00786 / 0.47 ( 8) link_ALPHA1-3 : angle 1.60893 / 0.99 ( 24) link_ALPHA1-6 : bond 0.00734 / 0.42 ( 8) link_ALPHA1-6 : angle 1.33662 / 0.80 ( 24) link_BETA1-4 : bond 0.00388 / 0.24 ( 40) link_BETA1-4 : angle 2.10582 / 1.46 ( 120) link_BETA1-6 : bond 0.00483 / 0.30 ( 8) link_BETA1-6 : angle 1.95780 / 1.14 ( 24) link_NAG-ASN : bond 0.00241 / 0.15 ( 24) link_NAG-ASN : angle 2.95249 / 1.97 ( 72) *********************** 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 265 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 240 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8494 (ptm-80) cc_final: 0.8234 (ptm160) REVERT: A 65 GLN cc_start: 0.8602 (mm-40) cc_final: 0.8301 (mt0) REVERT: L 27 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7430 (mtp85) REVERT: L 75 ILE cc_start: 0.9036 (mt) cc_final: 0.8680 (mt) REVERT: L 101 GLN cc_start: 0.8823 (mm110) cc_final: 0.8506 (pm20) REVERT: H 199 LYS cc_start: 0.8899 (tttt) cc_final: 0.8533 (ttpt) REVERT: H 400 ARG cc_start: 0.8454 (ptm-80) cc_final: 0.7660 (ptp90) REVERT: B 62 GLN cc_start: 0.8089 (mp10) cc_final: 0.7831 (mp10) REVERT: B 63 LYS cc_start: 0.8964 (ptmt) cc_final: 0.8590 (ptpp) REVERT: B 65 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8259 (tp40) REVERT: B 76 THR cc_start: 0.9071 (p) cc_final: 0.8865 (t) REVERT: B 123 LEU cc_start: 0.8894 (tp) cc_final: 0.8619 (tm) REVERT: M 20 THR cc_start: 0.8794 (p) cc_final: 0.8316 (t) REVERT: M 69 THR cc_start: 0.9000 (p) cc_final: 0.8696 (p) REVERT: M 82 ASP cc_start: 0.8852 (m-30) cc_final: 0.8228 (m-30) REVERT: M 107 ILE cc_start: 0.6885 (OUTLIER) cc_final: 0.6643 (pp) REVERT: I 141 ASN cc_start: 0.8842 (OUTLIER) cc_final: 0.8497 (t0) REVERT: I 465 ASN cc_start: 0.8593 (m-40) cc_final: 0.8214 (t0) REVERT: C 62 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.8058 (tp-100) REVERT: C 65 GLN cc_start: 0.8506 (mm-40) cc_final: 0.8297 (mm-40) REVERT: J 83 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7809 (tt0) REVERT: J 249 LYS cc_start: 0.8012 (ttpt) cc_final: 0.7365 (tmmt) REVERT: J 400 ARG cc_start: 0.8747 (ptm-80) cc_final: 0.8166 (ptm160) outliers start: 25 outliers final: 10 residues processed: 248 average time/residue: 0.5824 time to fit residues: 162.8858 Evaluate side-chains 217 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 204 time to evaluate : 0.726 ------------------------------------------------------------------------------- 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 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 49 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 347 HIS A 3 GLN ** A 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 N 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.069261 restraints weight = 32309.821| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.52 r_work: 0.2699 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 19184 Z= 0.353 Angle : 0.794 16.043 26225 Z= 0.396 Chirality : 0.051 0.222 3099 Planarity : 0.004 0.046 3189 Dihedral : 6.101 28.973 2461 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.92 % Favored : 95.90 % Rotamer: Outliers : 2.70 % Allowed : 9.55 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.17), residues: 2243 helix: 0.02 (0.95), residues: 24 sheet: 0.09 (0.17), residues: 895 loop : -0.37 (0.16), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 150 TYR 0.028 0.002 TYR G 121 PHE 0.018 0.002 PHE G 410 TRP 0.020 0.002 TRP I 115 HIS 0.007 0.002 HIS J 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00816 / 0.35 (19050) covalent geometry : angle 0.75590 / 0.39 (25865) SS BOND : bond 0.00575 / 0.36 ( 42) SS BOND : angle 1.40764 / 1.14 ( 84) hydrogen bonds : bond 0.04876 / 3.18 ( 573) hydrogen bonds : angle 6.92826 / 4.85 ( 1542) link_ALPHA1-2 : bond 0.00210 / 0.11 ( 4) link_ALPHA1-2 : angle 2.32772 / 1.18 ( 12) link_ALPHA1-3 : bond 0.00328 / 0.24 ( 8) link_ALPHA1-3 : angle 2.17123 / 1.32 ( 24) link_ALPHA1-6 : bond 0.00332 / 0.15 ( 8) link_ALPHA1-6 : angle 1.61570 / 0.97 ( 24) link_BETA1-4 : bond 0.00383 / 0.22 ( 40) link_BETA1-4 : angle 2.18302 / 1.47 ( 120) link_BETA1-6 : bond 0.00499 / 0.26 ( 8) link_BETA1-6 : angle 1.78589 / 1.02 ( 24) link_NAG-ASN : bond 0.00445 / 0.29 ( 24) link_NAG-ASN : angle 3.11252 / 2.07 ( 72) *********************** 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: 52 poor density : 204 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8614 (ptm-80) cc_final: 0.8092 (ptm-80) REVERT: A 65 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8486 (mm-40) REVERT: L 101 GLN cc_start: 0.8873 (mm110) cc_final: 0.8514 (pm20) REVERT: H 199 LYS cc_start: 0.8943 (tttt) cc_final: 0.8585 (ttpt) REVERT: H 230 CYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8689 (p) REVERT: H 400 ARG cc_start: 0.8504 (ptm-80) cc_final: 0.7645 (ptp90) REVERT: B 62 GLN cc_start: 0.8245 (mp10) cc_final: 0.7924 (mp10) REVERT: B 63 LYS cc_start: 0.9025 (ptmt) cc_final: 0.8726 (ptpp) REVERT: B 65 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8355 (tp40) REVERT: B 123 LEU cc_start: 0.8924 (tp) cc_final: 0.8633 (tm) REVERT: M 42 GLN cc_start: 0.8782 (mt0) cc_final: 0.8569 (mt0) REVERT: M 61 ARG cc_start: 0.8475 (ptt90) cc_final: 0.7960 (ptt-90) REVERT: M 69 THR cc_start: 0.9047 (p) cc_final: 0.8797 (p) REVERT: M 82 ASP cc_start: 0.8794 (m-30) cc_final: 0.8544 (m-30) REVERT: M 107 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6565 (pp) REVERT: I 465 ASN cc_start: 0.8639 (m-40) cc_final: 0.8272 (t0) REVERT: C 62 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.8031 (tp-100) REVERT: C 65 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8065 (mm-40) REVERT: J 141 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8475 (t0) REVERT: J 249 LYS cc_start: 0.8054 (ttpt) cc_final: 0.7374 (tmmt) REVERT: J 400 ARG cc_start: 0.8815 (ptm-80) cc_final: 0.8254 (ptm160) outliers start: 52 outliers final: 20 residues processed: 225 average time/residue: 0.5990 time to fit residues: 151.2371 Evaluate side-chains 210 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 81 GLU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 108 LEU 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 58 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 160 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 198 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 M 79 GLN ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 468 HIS C 120 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.095603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.072533 restraints weight = 31834.030| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.53 r_work: 0.2757 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19184 Z= 0.136 Angle : 0.642 9.330 26225 Z= 0.320 Chirality : 0.045 0.227 3099 Planarity : 0.003 0.043 3189 Dihedral : 5.503 30.719 2461 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.94 % Favored : 96.88 % Rotamer: Outliers : 1.66 % Allowed : 11.26 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2243 helix: -1.12 (0.80), residues: 28 sheet: 0.15 (0.17), residues: 903 loop : -0.34 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 150 TYR 0.014 0.001 TYR L 91 PHE 0.015 0.002 PHE H 410 TRP 0.019 0.001 TRP H 178 HIS 0.004 0.001 HIS J 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (19050) covalent geometry : angle 0.61348 / 0.32 (25865) SS BOND : bond 0.00317 / 0.20 ( 42) SS BOND : angle 0.83533 / 0.68 ( 84) hydrogen bonds : bond 0.03793 / 2.50 ( 573) hydrogen bonds : angle 6.44945 / 4.53 ( 1542) link_ALPHA1-2 : bond 0.00403 / 0.17 ( 4) link_ALPHA1-2 : angle 1.91390 / 0.98 ( 12) link_ALPHA1-3 : bond 0.00547 / 0.31 ( 8) link_ALPHA1-3 : angle 1.42293 / 0.85 ( 24) link_ALPHA1-6 : bond 0.00562 / 0.31 ( 8) link_ALPHA1-6 : angle 1.39163 / 0.83 ( 24) link_BETA1-4 : bond 0.00405 / 0.24 ( 40) link_BETA1-4 : angle 1.69829 / 1.14 ( 120) link_BETA1-6 : bond 0.00462 / 0.27 ( 8) link_BETA1-6 : angle 1.66790 / 0.96 ( 24) link_NAG-ASN : bond 0.00234 / 0.16 ( 24) link_NAG-ASN : angle 2.51986 / 1.67 ( 72) *********************** 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 238 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 206 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8525 (ptm-80) cc_final: 0.8029 (ptm-80) REVERT: G 432 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8537 (mp0) REVERT: A 13 ARG cc_start: 0.8786 (mmm-85) cc_final: 0.8490 (mmm-85) REVERT: A 107 ASP cc_start: 0.8743 (t0) cc_final: 0.8528 (t0) REVERT: L 27 ARG cc_start: 0.8165 (ttp80) cc_final: 0.7669 (mtp85) REVERT: L 101 GLN cc_start: 0.8851 (mm110) cc_final: 0.8478 (pm20) REVERT: H 199 LYS cc_start: 0.8860 (tttt) cc_final: 0.8416 (mtmt) REVERT: H 400 ARG cc_start: 0.8430 (ptm-80) cc_final: 0.7606 (ptp90) REVERT: B 3 GLN cc_start: 0.8491 (mm110) cc_final: 0.8009 (mm110) REVERT: B 62 GLN cc_start: 0.8107 (mp10) cc_final: 0.7819 (mp10) REVERT: B 63 LYS cc_start: 0.8955 (ptmt) cc_final: 0.8682 (ptpp) REVERT: B 65 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8192 (tp40) REVERT: B 123 LEU cc_start: 0.8969 (tp) cc_final: 0.8684 (tm) REVERT: M 61 ARG cc_start: 0.8564 (ptt90) cc_final: 0.8119 (ptt-90) REVERT: M 82 ASP cc_start: 0.8752 (m-30) cc_final: 0.8436 (m-30) REVERT: M 107 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6672 (pp) REVERT: I 465 ASN cc_start: 0.8584 (m-40) cc_final: 0.8288 (t0) REVERT: C 62 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8040 (tp-100) REVERT: C 65 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8313 (mm-40) REVERT: J 249 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7328 (tmmt) REVERT: J 400 ARG cc_start: 0.8778 (ptm-80) cc_final: 0.8240 (ptm160) outliers start: 32 outliers final: 13 residues processed: 221 average time/residue: 0.5959 time to fit residues: 147.8919 Evaluate side-chains 208 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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 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 81 GLU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain I residue 467 MET 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 J residue 230 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 109 optimal weight: 2.9990 chunk 135 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 137 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 47 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 HIS ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 468 HIS C 120 GLN N 79 GLN J 274 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.095009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.071952 restraints weight = 31812.870| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.52 r_work: 0.2754 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19184 Z= 0.171 Angle : 0.641 10.000 26225 Z= 0.318 Chirality : 0.045 0.225 3099 Planarity : 0.003 0.042 3189 Dihedral : 5.344 30.016 2460 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.39 % Favored : 96.43 % Rotamer: Outliers : 2.13 % Allowed : 11.62 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.17), residues: 2243 helix: -1.08 (0.78), residues: 28 sheet: 0.12 (0.17), residues: 898 loop : -0.32 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 150 TYR 0.017 0.001 TYR G 121 PHE 0.015 0.002 PHE H 410 TRP 0.016 0.001 TRP G 178 HIS 0.003 0.001 HIS G 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (19050) covalent geometry : angle 0.61185 / 0.31 (25865) SS BOND : bond 0.00336 / 0.20 ( 42) SS BOND : angle 0.79412 / 0.65 ( 84) hydrogen bonds : bond 0.03825 / 2.52 ( 573) hydrogen bonds : angle 6.35915 / 4.46 ( 1542) link_ALPHA1-2 : bond 0.00250 / 0.10 ( 4) link_ALPHA1-2 : angle 1.87278 / 0.95 ( 12) link_ALPHA1-3 : bond 0.00381 / 0.20 ( 8) link_ALPHA1-3 : angle 1.62912 / 0.97 ( 24) link_ALPHA1-6 : bond 0.00468 / 0.25 ( 8) link_ALPHA1-6 : angle 1.45585 / 0.87 ( 24) link_BETA1-4 : bond 0.00368 / 0.22 ( 40) link_BETA1-4 : angle 1.71207 / 1.14 ( 120) link_BETA1-6 : bond 0.00448 / 0.25 ( 8) link_BETA1-6 : angle 1.66353 / 0.96 ( 24) link_NAG-ASN : bond 0.00257 / 0.17 ( 24) link_NAG-ASN : angle 2.50603 / 1.65 ( 72) *********************** 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 239 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8576 (ptm-80) cc_final: 0.8274 (ptm-80) REVERT: G 432 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8583 (mp0) REVERT: L 27 ARG cc_start: 0.8124 (ttp80) cc_final: 0.7622 (mtp85) REVERT: L 61 ARG cc_start: 0.8999 (ptp90) cc_final: 0.8651 (ptp90) REVERT: L 101 GLN cc_start: 0.8881 (mm110) cc_final: 0.8496 (pm20) REVERT: H 199 LYS cc_start: 0.8869 (tttt) cc_final: 0.8443 (mtmt) REVERT: H 400 ARG cc_start: 0.8425 (ptm-80) cc_final: 0.7596 (ptp90) REVERT: B 3 GLN cc_start: 0.8504 (mm110) cc_final: 0.8017 (mm110) REVERT: B 62 GLN cc_start: 0.8112 (mp10) cc_final: 0.7803 (mp10) REVERT: B 63 LYS cc_start: 0.8977 (ptmt) cc_final: 0.8687 (ptpp) REVERT: B 65 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8135 (tp40) REVERT: B 123 LEU cc_start: 0.8974 (tp) cc_final: 0.8686 (tm) REVERT: M 61 ARG cc_start: 0.8558 (ptt90) cc_final: 0.8046 (ptt-90) REVERT: M 82 ASP cc_start: 0.8812 (m-30) cc_final: 0.8469 (m-30) REVERT: M 107 ILE cc_start: 0.6899 (OUTLIER) cc_final: 0.6655 (pp) REVERT: I 85 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7885 (mtm-85) REVERT: I 465 ASN cc_start: 0.8612 (m-40) cc_final: 0.8260 (t0) REVERT: C 10 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7665 (tt0) REVERT: C 23 LYS cc_start: 0.9122 (OUTLIER) cc_final: 0.8899 (tptt) REVERT: C 65 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8062 (mm-40) REVERT: N 81 GLU cc_start: 0.8805 (pt0) cc_final: 0.8584 (pt0) REVERT: J 249 LYS cc_start: 0.7997 (ttpt) cc_final: 0.7343 (tmmt) REVERT: J 400 ARG cc_start: 0.8797 (ptm-80) cc_final: 0.8269 (ptm160) outliers start: 41 outliers final: 20 residues processed: 219 average time/residue: 0.6385 time to fit residues: 156.7790 Evaluate side-chains 215 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 0.640 ------------------------------------------------------------------------------- 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 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 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 81 GLU Chi-restraints excluded: chain M residue 107 ILE Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 467 MET Chi-restraints excluded: chain C residue 10 GLU 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 C residue 35 THR Chi-restraints excluded: chain C residue 71 THR 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 38 optimal weight: 0.0970 chunk 181 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 HIS ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.094799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.071814 restraints weight = 31767.260| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.52 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: 0.8992 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19184 Z= 0.186 Angle : 0.646 10.492 26225 Z= 0.321 Chirality : 0.045 0.218 3099 Planarity : 0.003 0.042 3189 Dihedral : 5.301 28.983 2460 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.43 % Favored : 96.39 % Rotamer: Outliers : 2.23 % Allowed : 11.78 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2243 helix: -1.02 (0.79), residues: 28 sheet: 0.09 (0.17), residues: 898 loop : -0.30 (0.17), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 150 TYR 0.018 0.002 TYR G 121 PHE 0.014 0.002 PHE H 410 TRP 0.017 0.001 TRP G 178 HIS 0.003 0.001 HIS G 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (19050) covalent geometry : angle 0.61816 / 0.32 (25865) SS BOND : bond 0.00410 / 0.25 ( 42) SS BOND : angle 0.82006 / 0.68 ( 84) hydrogen bonds : bond 0.03828 / 2.52 ( 573) hydrogen bonds : angle 6.29680 / 4.42 ( 1542) link_ALPHA1-2 : bond 0.00222 / 0.09 ( 4) link_ALPHA1-2 : angle 1.88837 / 0.96 ( 12) link_ALPHA1-3 : bond 0.00347 / 0.18 ( 8) link_ALPHA1-3 : angle 1.65590 / 0.98 ( 24) link_ALPHA1-6 : bond 0.00437 / 0.23 ( 8) link_ALPHA1-6 : angle 1.48306 / 0.89 ( 24) link_BETA1-4 : bond 0.00343 / 0.20 ( 40) link_BETA1-4 : angle 1.68156 / 1.12 ( 120) link_BETA1-6 : bond 0.00441 / 0.25 ( 8) link_BETA1-6 : angle 1.64991 / 0.95 ( 24) link_NAG-ASN : bond 0.00309 / 0.20 ( 24) link_NAG-ASN : angle 2.45798 / 1.61 ( 72) *********************** 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 242 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8576 (ptm-80) cc_final: 0.8335 (ptm160) REVERT: G 432 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8620 (mp0) REVERT: A 13 ARG cc_start: 0.8764 (mmm-85) cc_final: 0.8455 (mmm-85) REVERT: L 27 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7653 (mtp85) REVERT: L 61 ARG cc_start: 0.9023 (ptp90) cc_final: 0.8650 (ptp90) REVERT: L 101 GLN cc_start: 0.8863 (mm110) cc_final: 0.8495 (pm20) REVERT: H 199 LYS cc_start: 0.8831 (tttt) cc_final: 0.8427 (mtmt) REVERT: H 400 ARG cc_start: 0.8405 (ptm-80) cc_final: 0.7564 (ptp90) REVERT: B 3 GLN cc_start: 0.8525 (mm110) cc_final: 0.8042 (mm110) REVERT: B 62 GLN cc_start: 0.8176 (mp10) cc_final: 0.7819 (mp10) REVERT: B 63 LYS cc_start: 0.9000 (ptmt) cc_final: 0.8709 (ptpp) REVERT: B 65 GLN cc_start: 0.8457 (mm-40) cc_final: 0.8206 (tp40) REVERT: B 123 LEU cc_start: 0.8961 (tp) cc_final: 0.8670 (tm) REVERT: M 61 ARG cc_start: 0.8554 (ptt90) cc_final: 0.8108 (ptt-90) REVERT: M 82 ASP cc_start: 0.8844 (m-30) cc_final: 0.8240 (m-30) REVERT: I 85 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7938 (mtm180) REVERT: I 465 ASN cc_start: 0.8605 (m-40) cc_final: 0.8266 (t0) REVERT: C 23 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8880 (tptt) REVERT: C 65 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8194 (mm-40) REVERT: N 31 ASP cc_start: 0.8907 (p0) cc_final: 0.8689 (p0) REVERT: J 249 LYS cc_start: 0.7986 (ttpt) cc_final: 0.7334 (tmmt) REVERT: J 400 ARG cc_start: 0.8782 (ptm-80) cc_final: 0.8258 (ptm160) outliers start: 43 outliers final: 29 residues processed: 223 average time/residue: 0.6095 time to fit residues: 152.9715 Evaluate side-chains 223 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 192 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 28 THR Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 59 ASN 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 319 SER 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 18 ARG Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain I residue 85 ARG Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 443 ILE 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 C residue 35 THR 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 148 optimal weight: 0.9990 chunk 104 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 86 optimal weight: 0.0060 chunk 46 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 chunk 140 optimal weight: 0.0980 chunk 106 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.096867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.073969 restraints weight = 31656.318| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.53 r_work: 0.2793 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19184 Z= 0.110 Angle : 0.599 11.072 26225 Z= 0.298 Chirality : 0.043 0.226 3099 Planarity : 0.003 0.041 3189 Dihedral : 5.033 26.937 2460 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.90 % Favored : 96.92 % Rotamer: Outliers : 1.87 % Allowed : 12.77 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.17), residues: 2243 helix: -1.07 (0.76), residues: 28 sheet: 0.15 (0.17), residues: 883 loop : -0.16 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 150 TYR 0.012 0.001 TYR G 121 PHE 0.013 0.001 PHE H 410 TRP 0.018 0.001 TRP I 178 HIS 0.003 0.001 HIS I 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (19050) covalent geometry : angle 0.57551 / 0.29 (25865) SS BOND : bond 0.00232 / 0.14 ( 42) SS BOND : angle 0.80013 / 0.61 ( 84) hydrogen bonds : bond 0.03396 / 2.25 ( 573) hydrogen bonds : angle 6.07968 / 4.27 ( 1542) link_ALPHA1-2 : bond 0.00420 / 0.18 ( 4) link_ALPHA1-2 : angle 1.72859 / 0.88 ( 12) link_ALPHA1-3 : bond 0.00526 / 0.30 ( 8) link_ALPHA1-3 : angle 1.39504 / 0.83 ( 24) link_ALPHA1-6 : bond 0.00525 / 0.29 ( 8) link_ALPHA1-6 : angle 1.39598 / 0.83 ( 24) link_BETA1-4 : bond 0.00402 / 0.25 ( 40) link_BETA1-4 : angle 1.50292 / 1.00 ( 120) link_BETA1-6 : bond 0.00444 / 0.25 ( 8) link_BETA1-6 : angle 1.59232 / 0.92 ( 24) link_NAG-ASN : bond 0.00198 / 0.13 ( 24) link_NAG-ASN : angle 2.17185 / 1.43 ( 72) *********************** 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 242 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 206 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8519 (ptm-80) cc_final: 0.8235 (ptm-80) REVERT: G 432 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8633 (mp0) REVERT: A 107 ASP cc_start: 0.8755 (t0) cc_final: 0.8546 (t0) REVERT: L 27 ARG cc_start: 0.8146 (ttp80) cc_final: 0.7638 (mtp85) REVERT: L 101 GLN cc_start: 0.8811 (mm110) cc_final: 0.8477 (pm20) REVERT: H 199 LYS cc_start: 0.8799 (tttt) cc_final: 0.8431 (mtmt) REVERT: H 400 ARG cc_start: 0.8336 (ptm-80) cc_final: 0.7475 (ptp90) REVERT: B 3 GLN cc_start: 0.8541 (mm110) cc_final: 0.8067 (mm110) REVERT: B 62 GLN cc_start: 0.8117 (mp10) cc_final: 0.7814 (mp10) REVERT: B 63 LYS cc_start: 0.8959 (ptmt) cc_final: 0.8663 (ptpp) REVERT: B 65 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8040 (tp40) REVERT: B 123 LEU cc_start: 0.8966 (tp) cc_final: 0.8680 (tm) REVERT: M 61 ARG cc_start: 0.8504 (ptt90) cc_final: 0.8058 (ptt-90) REVERT: M 82 ASP cc_start: 0.8861 (m-30) cc_final: 0.8527 (m-30) REVERT: I 465 ASN cc_start: 0.8595 (m-40) cc_final: 0.8289 (t0) REVERT: C 13 ARG cc_start: 0.8637 (mmm160) cc_final: 0.8350 (mmm-85) REVERT: C 23 LYS cc_start: 0.9117 (OUTLIER) cc_final: 0.8894 (tptt) REVERT: C 62 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.8058 (tp-100) REVERT: C 65 GLN cc_start: 0.8654 (mm-40) cc_final: 0.8328 (mm-40) REVERT: C 76 THR cc_start: 0.9106 (p) cc_final: 0.8853 (t) REVERT: C 87 ARG cc_start: 0.6542 (mpt180) cc_final: 0.6309 (mpt180) REVERT: C 90 ASP cc_start: 0.8323 (m-30) cc_final: 0.8085 (m-30) REVERT: J 249 LYS cc_start: 0.7925 (ttpt) cc_final: 0.7283 (tmmt) REVERT: J 400 ARG cc_start: 0.8722 (ptm-80) cc_final: 0.8212 (ptm160) outliers start: 36 outliers final: 21 residues processed: 228 average time/residue: 0.5789 time to fit residues: 148.3945 Evaluate side-chains 219 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 4 MET Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 319 SER 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 I residue 400 ARG 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 C residue 35 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 89 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 chunk 64 optimal weight: 0.2980 chunk 121 optimal weight: 10.0000 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 274 HIS ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN M 70 GLN ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN N 90 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.071240 restraints weight = 31925.401| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.53 r_work: 0.2738 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 19184 Z= 0.250 Angle : 0.678 10.957 26225 Z= 0.337 Chirality : 0.046 0.206 3099 Planarity : 0.004 0.047 3189 Dihedral : 5.305 27.591 2460 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.79 % Favored : 96.03 % Rotamer: Outliers : 2.49 % Allowed : 12.77 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.17), residues: 2243 helix: -0.90 (0.80), residues: 28 sheet: 0.02 (0.17), residues: 906 loop : -0.30 (0.17), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 150 TYR 0.021 0.002 TYR G 121 PHE 0.015 0.002 PHE H 410 TRP 0.015 0.002 TRP G 178 HIS 0.004 0.001 HIS G 191 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.25 (19050) covalent geometry : angle 0.65050 / 0.33 (25865) SS BOND : bond 0.00395 / 0.24 ( 42) SS BOND : angle 1.01861 / 0.81 ( 84) hydrogen bonds : bond 0.04024 / 2.64 ( 573) hydrogen bonds : angle 6.34856 / 4.44 ( 1542) link_ALPHA1-2 : bond 0.00142 / 0.06 ( 4) link_ALPHA1-2 : angle 1.88682 / 0.96 ( 12) link_ALPHA1-3 : bond 0.00207 / 0.12 ( 8) link_ALPHA1-3 : angle 1.81757 / 1.07 ( 24) link_ALPHA1-6 : bond 0.00357 / 0.17 ( 8) link_ALPHA1-6 : angle 1.52419 / 0.91 ( 24) link_BETA1-4 : bond 0.00318 / 0.19 ( 40) link_BETA1-4 : angle 1.69789 / 1.12 ( 120) link_BETA1-6 : bond 0.00436 / 0.23 ( 8) link_BETA1-6 : angle 1.62870 / 0.95 ( 24) link_NAG-ASN : bond 0.00370 / 0.24 ( 24) link_NAG-ASN : angle 2.48216 / 1.62 ( 72) *********************** 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 250 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 202 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8605 (ptm-80) cc_final: 0.8290 (ptm-80) REVERT: G 432 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8664 (mp0) REVERT: A 23 LYS cc_start: 0.8772 (tttm) cc_final: 0.8488 (ttpt) REVERT: A 26 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: L 27 ARG cc_start: 0.8170 (ttp80) cc_final: 0.7636 (mtp85) REVERT: L 101 GLN cc_start: 0.8880 (mm110) cc_final: 0.8506 (pm20) REVERT: H 199 LYS cc_start: 0.8837 (tttt) cc_final: 0.8424 (mtmt) REVERT: H 261 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8386 (tmtt) REVERT: H 400 ARG cc_start: 0.8392 (ptm-80) cc_final: 0.7522 (ptp90) REVERT: B 3 GLN cc_start: 0.8576 (mm110) cc_final: 0.8070 (mm110) REVERT: B 62 GLN cc_start: 0.8241 (mp10) cc_final: 0.7877 (mp10) REVERT: B 63 LYS cc_start: 0.9023 (ptmt) cc_final: 0.8712 (ptpp) REVERT: B 65 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8225 (tp40) REVERT: B 123 LEU cc_start: 0.8949 (tp) cc_final: 0.8646 (tm) REVERT: M 61 ARG cc_start: 0.8500 (ptt90) cc_final: 0.8006 (ptt-90) REVERT: M 82 ASP cc_start: 0.8878 (m-30) cc_final: 0.8262 (m-30) REVERT: I 465 ASN cc_start: 0.8624 (m-40) cc_final: 0.8281 (t0) REVERT: C 23 LYS cc_start: 0.9083 (OUTLIER) cc_final: 0.8853 (tptt) REVERT: C 62 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.8052 (tp-100) REVERT: C 65 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8193 (mm-40) REVERT: C 76 THR cc_start: 0.9104 (p) cc_final: 0.8903 (t) REVERT: C 87 ARG cc_start: 0.6623 (mpt180) cc_final: 0.6376 (mpt180) REVERT: J 227 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: J 249 LYS cc_start: 0.8016 (ttpt) cc_final: 0.7352 (tmmt) REVERT: J 400 ARG cc_start: 0.8793 (ptm-80) cc_final: 0.8274 (ptm160) outliers start: 48 outliers final: 30 residues processed: 228 average time/residue: 0.6244 time to fit residues: 160.3478 Evaluate side-chains 232 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 26 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 63 LYS 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 4 MET Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 261 LYS Chi-restraints excluded: chain H residue 319 SER 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 18 ARG 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 I residue 141 ASN Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 400 ARG Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 20 THR Chi-restraints excluded: chain N residue 52 SER 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 22 optimal weight: 0.8980 chunk 188 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN L 90 HIS M 70 GLN ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 468 HIS C 120 GLN N 90 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.094455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.071466 restraints weight = 31764.978| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.51 r_work: 0.2742 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8997 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 19184 Z= 0.223 Angle : 0.668 11.637 26225 Z= 0.332 Chirality : 0.046 0.207 3099 Planarity : 0.004 0.052 3189 Dihedral : 5.311 27.622 2460 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.70 % Favored : 96.12 % Rotamer: Outliers : 2.13 % Allowed : 13.44 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.17), residues: 2243 helix: -0.94 (0.80), residues: 28 sheet: 0.07 (0.17), residues: 896 loop : -0.38 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 150 TYR 0.019 0.002 TYR G 121 PHE 0.016 0.002 PHE H 410 TRP 0.017 0.002 TRP G 178 HIS 0.004 0.001 HIS I 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (19050) covalent geometry : angle 0.64140 / 0.33 (25865) SS BOND : bond 0.00385 / 0.24 ( 42) SS BOND : angle 0.98667 / 0.77 ( 84) hydrogen bonds : bond 0.03939 / 2.59 ( 573) hydrogen bonds : angle 6.32863 / 4.43 ( 1542) link_ALPHA1-2 : bond 0.00142 / 0.06 ( 4) link_ALPHA1-2 : angle 1.93486 / 0.98 ( 12) link_ALPHA1-3 : bond 0.00259 / 0.13 ( 8) link_ALPHA1-3 : angle 1.74842 / 1.03 ( 24) link_ALPHA1-6 : bond 0.00382 / 0.19 ( 8) link_ALPHA1-6 : angle 1.50625 / 0.90 ( 24) link_BETA1-4 : bond 0.00321 / 0.19 ( 40) link_BETA1-4 : angle 1.64943 / 1.08 ( 120) link_BETA1-6 : bond 0.00430 / 0.23 ( 8) link_BETA1-6 : angle 1.61709 / 0.93 ( 24) link_NAG-ASN : bond 0.00351 / 0.23 ( 24) link_NAG-ASN : angle 2.43931 / 1.60 ( 72) *********************** 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 237 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 196 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8612 (ptm-80) cc_final: 0.8307 (ptm-80) REVERT: G 432 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8668 (mp0) REVERT: A 23 LYS cc_start: 0.8793 (tttm) cc_final: 0.8503 (ttpt) REVERT: A 26 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: L 27 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7550 (mtp85) REVERT: L 101 GLN cc_start: 0.8876 (mm110) cc_final: 0.8519 (pm20) REVERT: H 199 LYS cc_start: 0.8780 (tttt) cc_final: 0.8371 (mtmt) REVERT: H 261 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8364 (tmtt) REVERT: H 400 ARG cc_start: 0.8398 (ptm-80) cc_final: 0.7526 (ptp90) REVERT: B 3 GLN cc_start: 0.8555 (mm110) cc_final: 0.8060 (mm110) REVERT: B 62 GLN cc_start: 0.8242 (mp10) cc_final: 0.7884 (mp10) REVERT: B 63 LYS cc_start: 0.9003 (ptmt) cc_final: 0.8739 (ptpp) REVERT: B 65 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8170 (tp40) REVERT: B 123 LEU cc_start: 0.8948 (tp) cc_final: 0.8644 (tm) REVERT: M 61 ARG cc_start: 0.8541 (ptt90) cc_final: 0.8054 (ptt-90) REVERT: M 82 ASP cc_start: 0.8872 (m-30) cc_final: 0.8243 (m-30) REVERT: I 465 ASN cc_start: 0.8617 (m-40) cc_final: 0.8284 (t0) REVERT: C 23 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8858 (tptt) REVERT: C 62 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8051 (tp-100) REVERT: C 65 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8218 (mm-40) REVERT: J 249 LYS cc_start: 0.8003 (ttpt) cc_final: 0.7322 (tmmt) REVERT: J 400 ARG cc_start: 0.8788 (ptm-80) cc_final: 0.8261 (ptm160) outliers start: 41 outliers final: 27 residues processed: 218 average time/residue: 0.6405 time to fit residues: 156.9383 Evaluate side-chains 226 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 195 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 26 GLU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 63 LYS 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 4 MET Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain H residue 261 LYS 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 18 ARG Chi-restraints excluded: chain M residue 56 THR 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 23 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain N residue 5 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 123 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN L 90 HIS ** I 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 468 HIS ** 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 = 0.3309 r_free = 0.3309 target = 0.095375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.072482 restraints weight = 31634.778| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.51 r_work: 0.2764 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19184 Z= 0.157 Angle : 0.634 11.674 26225 Z= 0.315 Chirality : 0.045 0.213 3099 Planarity : 0.003 0.055 3189 Dihedral : 5.184 26.759 2460 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.21 % Rotamer: Outliers : 1.76 % Allowed : 13.91 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.17), residues: 2243 helix: -1.05 (0.76), residues: 28 sheet: 0.10 (0.17), residues: 896 loop : -0.32 (0.17), residues: 1319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 150 TYR 0.017 0.001 TYR C 32 PHE 0.014 0.002 PHE H 410 TRP 0.018 0.001 TRP G 178 HIS 0.003 0.001 HIS N 90 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (19050) covalent geometry : angle 0.60931 / 0.31 (25865) SS BOND : bond 0.00427 / 0.30 ( 42) SS BOND : angle 0.84085 / 0.67 ( 84) hydrogen bonds : bond 0.03664 / 2.42 ( 573) hydrogen bonds : angle 6.21782 / 4.36 ( 1542) link_ALPHA1-2 : bond 0.00247 / 0.10 ( 4) link_ALPHA1-2 : angle 1.86731 / 0.94 ( 12) link_ALPHA1-3 : bond 0.00392 / 0.21 ( 8) link_ALPHA1-3 : angle 1.56508 / 0.92 ( 24) link_ALPHA1-6 : bond 0.00459 / 0.24 ( 8) link_ALPHA1-6 : angle 1.45072 / 0.87 ( 24) link_BETA1-4 : bond 0.00352 / 0.21 ( 40) link_BETA1-4 : angle 1.54339 / 1.01 ( 120) link_BETA1-6 : bond 0.00431 / 0.24 ( 8) link_BETA1-6 : angle 1.58411 / 0.91 ( 24) link_NAG-ASN : bond 0.00255 / 0.17 ( 24) link_NAG-ASN : angle 2.29278 / 1.50 ( 72) ********************** 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 231 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 400 ARG cc_start: 0.8596 (ptm-80) cc_final: 0.8290 (ptm-80) REVERT: G 432 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8628 (mp0) REVERT: A 23 LYS cc_start: 0.8782 (tttm) cc_final: 0.8490 (ttpt) REVERT: A 26 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: L 27 ARG cc_start: 0.8155 (ttp80) cc_final: 0.7600 (mtp85) REVERT: L 101 GLN cc_start: 0.8798 (mm110) cc_final: 0.8479 (pm20) REVERT: H 199 LYS cc_start: 0.8795 (tttt) cc_final: 0.8392 (mtmt) REVERT: H 261 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8350 (tmtt) REVERT: H 400 ARG cc_start: 0.8375 (ptm-80) cc_final: 0.7516 (ptp90) REVERT: B 3 GLN cc_start: 0.8554 (mm110) cc_final: 0.8166 (mm110) REVERT: B 62 GLN cc_start: 0.8179 (mp10) cc_final: 0.7859 (mp10) REVERT: B 63 LYS cc_start: 0.8981 (ptmt) cc_final: 0.8662 (ptpp) REVERT: B 65 GLN cc_start: 0.8453 (mm-40) cc_final: 0.8178 (tp40) REVERT: B 123 LEU cc_start: 0.8945 (tp) cc_final: 0.8642 (tm) REVERT: M 61 ARG cc_start: 0.8545 (ptt90) cc_final: 0.8088 (ptt-90) REVERT: M 82 ASP cc_start: 0.8872 (m-30) cc_final: 0.8246 (m-30) REVERT: I 465 ASN cc_start: 0.8616 (m-40) cc_final: 0.8289 (t0) REVERT: C 23 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8866 (tptt) REVERT: C 62 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.8054 (tp-100) REVERT: C 65 GLN cc_start: 0.8632 (mm-40) cc_final: 0.8237 (mm-40) REVERT: J 249 LYS cc_start: 0.7971 (ttpt) cc_final: 0.7311 (tmmt) REVERT: J 400 ARG cc_start: 0.8775 (ptm-80) cc_final: 0.8247 (ptm160) outliers start: 34 outliers final: 25 residues processed: 214 average time/residue: 0.5848 time to fit residues: 140.9857 Evaluate side-chains 222 residues out of total 1927 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.679 ------------------------------------------------------------------------------- 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 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 4 MET 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 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 18 ARG Chi-restraints excluded: chain M residue 69 THR 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 23 LYS Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain N residue 5 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 135 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 83 optimal weight: 0.0040 chunk 152 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 3 GLN L 90 HIS M 38 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.094260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.071265 restraints weight = 32105.910| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.52 r_work: 0.2740 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9001 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 19184 Z= 0.244 Angle : 0.692 11.800 26225 Z= 0.343 Chirality : 0.047 0.256 3099 Planarity : 0.004 0.053 3189 Dihedral : 5.346 29.516 2460 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.74 % Favored : 96.08 % Rotamer: Outliers : 1.87 % Allowed : 13.75 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.28 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.17), residues: 2243 helix: -0.89 (0.80), residues: 28 sheet: 0.00 (0.17), residues: 904 loop : -0.39 (0.17), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 150 TYR 0.020 0.002 TYR G 121 PHE 0.016 0.002 PHE H 410 TRP 0.016 0.002 TRP G 178 HIS 0.006 0.001 HIS H 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 (19050) covalent geometry : angle 0.66297 / 0.34 (25865) SS BOND : bond 0.00384 / 0.23 ( 42) SS BOND : angle 1.55298 / 1.09 ( 84) hydrogen bonds : bond 0.04000 / 2.63 ( 573) hydrogen bonds : angle 6.36033 / 4.45 ( 1542) link_ALPHA1-2 : bond 0.00120 / 0.05 ( 4) link_ALPHA1-2 : angle 1.91487 / 0.97 ( 12) link_ALPHA1-3 : bond 0.00240 / 0.13 ( 8) link_ALPHA1-3 : angle 1.80288 / 1.06 ( 24) link_ALPHA1-6 : bond 0.00375 / 0.18 ( 8) link_ALPHA1-6 : angle 1.50729 / 0.90 ( 24) link_BETA1-4 : bond 0.00322 / 0.19 ( 40) link_BETA1-4 : angle 1.64614 / 1.08 ( 120) link_BETA1-6 : bond 0.00431 / 0.23 ( 8) link_BETA1-6 : angle 1.61609 / 0.93 ( 24) link_NAG-ASN : bond 0.00369 / 0.24 ( 24) link_NAG-ASN : angle 2.44411 / 1.60 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6163.52 seconds wall clock time: 106 minutes 13.60 seconds (6373.60 seconds total)