Starting phenix.real_space_refine on Mon Jun 16 12:42:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g3o_29706/06_2025/8g3o_29706.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g3o_29706/06_2025/8g3o_29706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8g3o_29706/06_2025/8g3o_29706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g3o_29706/06_2025/8g3o_29706.map" model { file = "/net/cci-nas-00/data/ceres_data/8g3o_29706/06_2025/8g3o_29706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g3o_29706/06_2025/8g3o_29706.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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 11416 2.51 5 N 3132 2.21 5 O 3825 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 139 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18487 Number of models: 1 Model: "" Number of chains: 38 Chain: "E" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "F" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "D" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} Chain: "C" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "I" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 104} 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: "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: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "k" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "s" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "3" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "t" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "w" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "1" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "4" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "5" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "7" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "u" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" 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: 13.58, per 1000 atoms: 0.73 Number of scatterers: 18487 At special positions: 0 Unit cell: (112.88, 140.27, 170.15, 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 3825 8.00 N 3132 7.00 C 11416 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.06 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.06 Simple disulfide: pdb=" SG CYS G 92 " - pdb=" SG CYS G 417 " distance=2.07 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=2.06 Simple disulfide: pdb=" SG CYS G 183 " - pdb=" SG CYS G 230 " distance=2.06 Simple disulfide: pdb=" SG CYS G 232 " - pdb=" SG CYS G 237 " distance=2.08 Simple disulfide: pdb=" SG CYS G 278 " - pdb=" SG CYS G 291 " distance=2.06 Simple disulfide: pdb=" SG CYS G 280 " - pdb=" SG CYS G 289 " distance=2.07 Simple disulfide: pdb=" SG CYS G 318 " - pdb=" SG CYS G 337 " distance=2.10 Simple disulfide: pdb=" SG CYS G 421 " - pdb=" SG CYS G 447 " distance=2.13 Simple disulfide: pdb=" SG CYS H 92 " - pdb=" SG CYS H 417 " distance=2.06 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=2.05 Simple disulfide: pdb=" SG CYS H 183 " - pdb=" SG CYS H 230 " distance=2.02 Simple disulfide: pdb=" SG CYS H 232 " - pdb=" SG CYS H 237 " distance=2.09 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=2.08 Simple disulfide: pdb=" SG CYS H 318 " - pdb=" SG CYS H 337 " distance=2.08 Simple disulfide: pdb=" SG CYS H 421 " - pdb=" SG CYS H 447 " distance=2.12 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.05 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.07 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.06 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.06 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.07 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.06 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.07 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.08 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.13 Simple disulfide: pdb=" SG CYS J 92 " - pdb=" SG CYS J 417 " distance=2.05 Simple disulfide: pdb=" SG CYS J 124 " - pdb=" SG CYS J 129 " distance=2.09 Simple disulfide: pdb=" SG CYS J 175 " - pdb=" SG CYS J 193 " distance=2.06 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=2.08 Simple disulfide: pdb=" SG CYS J 278 " - pdb=" SG CYS J 291 " distance=2.05 Simple disulfide: pdb=" SG CYS J 280 " - pdb=" SG CYS J 289 " distance=2.10 Simple disulfide: pdb=" SG CYS J 318 " - pdb=" SG CYS J 337 " distance=2.09 Simple disulfide: pdb=" SG CYS J 421 " - pdb=" SG CYS J 447 " distance=2.12 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 k 3 " - " MAN k 6 " " MAN k 6 " - " MAN k 8 " " BMA s 3 " - " MAN s 6 " " MAN s 6 " - " MAN s 8 " BETA1-4 " NAG 1 1 " - " NAG 1 2 " " NAG 2 1 " - " NAG 2 2 " " NAG 3 1 " - " NAG 3 2 " " NAG 3 2 " - " BMA 3 3 " " NAG 4 1 " - " NAG 4 2 " " NAG 5 1 " - " NAG 5 2 " " NAG 7 1 " - " NAG 7 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG g 1 " - " NAG g 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG o 1 " - " NAG o 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " " NAG t 1 " - " NAG t 2 " " NAG u 1 " - " NAG u 2 " " NAG w 1 " - " NAG w 2 " BETA1-6 " NAG 5 1 " - " FUC 5 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG e 1 " - " FUC e 3 " " NAG m 1 " - " FUC m 3 " " 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 B 86 " " NAG r 1 " - " ASN B 146 " " NAG s 1 " - " ASN B 200 " " NAG t 1 " - " ASN B 234 " " NAG u 1 " - " ASN B 245 " " NAG w 1 " - " ASN B 367 " Time building additional restraints: 6.27 Conformation dependent library (CDL) restraints added in 2.5 seconds 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4108 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 42 sheets defined 4.7% alpha, 41.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.68 Creating SS restraints... Processing helix chain 'E' and resid 62 through 65 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.792A pdb=" N SER F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 87 through 91 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.780A pdb=" N SER D 83 " --> pdb=" O SER D 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.785A pdb=" N SER I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 110 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.736A pdb=" N ASN G 146 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 252 Processing helix chain 'H' and resid 104 through 110 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.740A pdb=" N ASN H 146 " --> pdb=" O VAL H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 252 Processing helix chain 'B' and resid 104 through 110 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.739A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'J' and resid 104 through 110 Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.731A pdb=" N ASN J 146 " --> pdb=" O VAL J 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.462A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.462A pdb=" N GLU E 10 " --> pdb=" O THR E 125 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYS E 96 " --> pdb=" O TRP E 118 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TRP E 118 " --> pdb=" O CYS E 96 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG E 98 " --> pdb=" O ALA E 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.629A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.582A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (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: 6.479A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.747A 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: 6.479A pdb=" N GLU A 10 " --> pdb=" O THR A 125 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS A 96 " --> pdb=" O TRP A 118 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N TRP A 118 " --> pdb=" O CYS A 96 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG A 98 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 104 through 105 Processing sheet with id=AB2, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.632A pdb=" N GLU D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.595A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.482A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.482A pdb=" N GLU C 10 " --> pdb=" O THR C 125 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS C 96 " --> pdb=" O TRP C 118 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP C 118 " --> pdb=" O CYS C 96 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG C 98 " --> pdb=" O ALA C 116 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 104 through 105 Processing sheet with id=AB8, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.631A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.573A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 96 through 102 removed outlier: 5.470A pdb=" N PHE G 97 " --> pdb=" O THR G 449 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR G 449 " --> pdb=" O PHE G 97 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N CYS G 447 " --> pdb=" O PRO G 99 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ARG G 420 " --> pdb=" O GLY G 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 115 through 124 removed outlier: 4.802A pdb=" N TRP G 115 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N THR G 138 " --> pdb=" O TRP G 115 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR G 117 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN G 136 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU G 119 " --> pdb=" O LEU G 134 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU G 134 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N THR G 157 " --> pdb=" O GLY G 135 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU G 158 " --> pdb=" O VAL G 174 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS G 172 " --> pdb=" O MET G 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 179 through 184 removed outlier: 4.129A pdb=" N ASP G 197 " --> pdb=" O ASN G 200 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR G 207 " --> pdb=" O LEU G 211 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU G 211 " --> pdb=" O TYR G 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 231 through 233 removed outlier: 6.447A pdb=" N GLU G 258 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE G 262 " --> pdb=" O GLU G 258 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 276 through 283 removed outlier: 5.414A pdb=" N GLU G 277 " --> pdb=" O ARG G 292 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ARG G 292 " --> pdb=" O GLU G 277 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 352 through 356 removed outlier: 4.485A pdb=" N TRP G 352 " --> pdb=" O GLY G 363 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP G 402 " --> pdb=" O GLY G 373 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N GLU G 375 " --> pdb=" O ARG G 400 " (cutoff:3.500A) removed outlier: 10.452A pdb=" N ARG G 400 " --> pdb=" O GLU G 375 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N PHE G 377 " --> pdb=" O VAL G 398 " (cutoff:3.500A) removed outlier: 13.554A pdb=" N VAL G 398 " --> pdb=" O PHE G 377 " (cutoff:3.500A) removed outlier: 15.764A pdb=" N VAL G 379 " --> pdb=" O VAL G 396 " (cutoff:3.500A) removed outlier: 16.338A pdb=" N VAL G 396 " --> pdb=" O VAL G 379 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 96 through 102 removed outlier: 3.782A pdb=" N GLY H 96 " --> pdb=" O THR H 449 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL H 445 " --> pdb=" O PHE H 100 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS H 102 " --> pdb=" O ILE H 443 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE H 443 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG H 420 " --> pdb=" O GLY H 448 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 115 through 124 removed outlier: 4.778A pdb=" N TRP H 115 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N THR H 138 " --> pdb=" O TRP H 115 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N THR H 117 " --> pdb=" O GLN H 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN H 136 " --> pdb=" O THR H 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU H 119 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU H 134 " --> pdb=" O GLU H 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR H 157 " --> pdb=" O GLY H 135 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU H 158 " --> pdb=" O VAL H 174 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS H 172 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 179 through 184 removed outlier: 4.121A pdb=" N ASP H 197 " --> pdb=" O ASN H 200 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR H 207 " --> pdb=" O LEU H 211 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU H 211 " --> pdb=" O TYR H 207 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 231 through 233 removed outlier: 6.427A pdb=" N GLU H 258 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE H 262 " --> pdb=" O GLU H 258 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 276 through 283 removed outlier: 5.404A pdb=" N GLU H 277 " --> pdb=" O ARG H 292 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG H 292 " --> pdb=" O GLU H 277 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 352 through 356 removed outlier: 4.461A pdb=" N TRP H 352 " --> pdb=" O GLY H 363 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP H 402 " --> pdb=" O GLY H 373 " (cutoff:3.500A) removed outlier: 9.717A pdb=" N GLU H 375 " --> pdb=" O ARG H 400 " (cutoff:3.500A) removed outlier: 10.503A pdb=" N ARG H 400 " --> pdb=" O GLU H 375 " (cutoff:3.500A) removed outlier: 11.513A pdb=" N PHE H 377 " --> pdb=" O VAL H 398 " (cutoff:3.500A) removed outlier: 13.543A pdb=" N VAL H 398 " --> pdb=" O PHE H 377 " (cutoff:3.500A) removed outlier: 15.750A pdb=" N VAL H 379 " --> pdb=" O VAL H 396 " (cutoff:3.500A) removed outlier: 16.346A pdb=" N VAL H 396 " --> pdb=" O VAL H 379 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 96 through 102 removed outlier: 5.479A pdb=" N PHE B 97 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N THR B 449 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N CYS B 447 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 115 through 124 removed outlier: 4.772A pdb=" N TRP B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR B 138 " --> pdb=" O TRP B 115 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 157 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 158 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS B 172 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 179 through 184 removed outlier: 4.123A pdb=" N ASP B 197 " --> pdb=" O ASN B 200 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 231 through 233 removed outlier: 6.429A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 276 through 283 removed outlier: 5.424A pdb=" N GLU B 277 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ARG B 292 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 352 through 356 removed outlier: 4.494A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ASP B 402 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N GLU B 375 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 10.486A pdb=" N ARG B 400 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 11.509A pdb=" N PHE B 377 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 13.562A pdb=" N VAL B 398 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 15.815A pdb=" N VAL B 379 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 16.373A pdb=" N VAL B 396 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 96 through 102 removed outlier: 3.796A pdb=" N GLY J 96 " --> pdb=" O THR J 449 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL J 445 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS J 102 " --> pdb=" O ILE J 443 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE J 443 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG J 420 " --> pdb=" O GLY J 448 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 115 through 124 removed outlier: 4.798A pdb=" N TRP J 115 " --> pdb=" O THR J 138 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N THR J 138 " --> pdb=" O TRP J 115 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N THR J 117 " --> pdb=" O GLN J 136 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLN J 136 " --> pdb=" O THR J 117 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLU J 119 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU J 134 " --> pdb=" O GLU J 119 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR J 157 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU J 158 " --> pdb=" O VAL J 174 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS J 172 " --> pdb=" O MET J 160 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 179 through 184 removed outlier: 4.117A 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: 5.180A pdb=" N LEU J 211 " --> pdb=" O TYR J 207 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 231 through 233 removed outlier: 6.435A pdb=" N GLU J 258 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ILE J 262 " --> pdb=" O GLU J 258 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 276 through 283 removed outlier: 5.405A pdb=" N GLU J 277 " --> pdb=" O ARG J 292 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG J 292 " --> pdb=" O GLU J 277 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 352 through 356 removed outlier: 4.458A pdb=" N TRP J 352 " --> pdb=" O GLY J 363 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ASP J 402 " --> pdb=" O GLY J 373 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N GLU J 375 " --> pdb=" O ARG J 400 " (cutoff:3.500A) removed outlier: 10.429A pdb=" N ARG J 400 " --> pdb=" O GLU J 375 " (cutoff:3.500A) removed outlier: 11.508A pdb=" N PHE J 377 " --> pdb=" O VAL J 398 " (cutoff:3.500A) removed outlier: 13.570A pdb=" N VAL J 398 " --> pdb=" O PHE J 377 " (cutoff:3.500A) removed outlier: 15.789A pdb=" N VAL J 379 " --> pdb=" O VAL J 396 " (cutoff:3.500A) removed outlier: 16.357A pdb=" N VAL J 396 " --> pdb=" O VAL J 379 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.55 Time building geometry restraints manager: 7.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3171 1.32 - 1.45: 5346 1.45 - 1.58: 10224 1.58 - 1.71: 0 1.71 - 1.85: 134 Bond restraints: 18875 Sorted by residual: bond pdb=" C SER J 404 " pdb=" O SER J 404 " ideal model delta sigma weight residual 1.235 1.298 -0.062 1.26e-02 6.30e+03 2.45e+01 bond pdb=" C LYS G 350 " pdb=" O LYS G 350 " ideal model delta sigma weight residual 1.235 1.288 -0.053 1.20e-02 6.94e+03 1.97e+01 bond pdb=" N GLY J 286 " pdb=" CA GLY J 286 " ideal model delta sigma weight residual 1.442 1.475 -0.033 7.70e-03 1.69e+04 1.87e+01 bond pdb=" N GLY G 286 " pdb=" CA GLY G 286 " ideal model delta sigma weight residual 1.442 1.474 -0.032 7.70e-03 1.69e+04 1.77e+01 bond pdb=" C PRO H 90 " pdb=" O PRO H 90 " ideal model delta sigma weight residual 1.233 1.184 0.049 1.18e-02 7.18e+03 1.73e+01 ... (remaining 18870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 20936 2.21 - 4.42: 4275 4.42 - 6.63: 365 6.63 - 8.84: 33 8.84 - 11.04: 8 Bond angle restraints: 25617 Sorted by residual: angle pdb=" N ILE J 397 " pdb=" CA ILE J 397 " pdb=" C ILE J 397 " ideal model delta sigma weight residual 111.81 106.63 5.18 8.60e-01 1.35e+00 3.63e+01 angle pdb=" N ILE B 397 " pdb=" CA ILE B 397 " pdb=" C ILE B 397 " ideal model delta sigma weight residual 111.81 106.70 5.11 8.60e-01 1.35e+00 3.53e+01 angle pdb=" N LYS J 128 " pdb=" CA LYS J 128 " pdb=" CB LYS J 128 " ideal model delta sigma weight residual 111.52 100.48 11.04 1.86e+00 2.89e-01 3.53e+01 angle pdb=" N ILE G 397 " pdb=" CA ILE G 397 " pdb=" C ILE G 397 " ideal model delta sigma weight residual 111.81 106.77 5.04 8.60e-01 1.35e+00 3.43e+01 angle pdb=" CA ASP H 125 " pdb=" CB ASP H 125 " pdb=" CG ASP H 125 " ideal model delta sigma weight residual 112.60 118.41 -5.81 1.00e+00 1.00e+00 3.38e+01 ... (remaining 25612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.75: 11476 19.75 - 39.50: 466 39.50 - 59.25: 107 59.25 - 79.00: 55 79.00 - 98.75: 27 Dihedral angle restraints: 12131 sinusoidal: 5680 harmonic: 6451 Sorted by residual: dihedral pdb=" CA GLY J 244 " pdb=" C GLY J 244 " pdb=" N ASN J 245 " pdb=" CA ASN J 245 " ideal model delta harmonic sigma weight residual -180.00 -150.08 -29.92 0 5.00e+00 4.00e-02 3.58e+01 dihedral pdb=" CA ASP J 127 " pdb=" C ASP J 127 " pdb=" N LYS J 128 " pdb=" CA LYS J 128 " ideal model delta harmonic sigma weight residual -180.00 -155.41 -24.59 0 5.00e+00 4.00e-02 2.42e+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 180.00 155.95 24.05 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 12128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 2423 0.120 - 0.240: 576 0.240 - 0.361: 11 0.361 - 0.481: 5 0.481 - 0.601: 1 Chirality restraints: 3016 Sorted by residual: chirality pdb=" C1 BMA k 3 " pdb=" O4 NAG k 2 " pdb=" C2 BMA k 3 " pdb=" O5 BMA k 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.21e+01 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 2.23 0.17 2.00e-02 2.50e+03 6.96e+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 2.25 0.15 2.00e-02 2.50e+03 5.46e+01 ... (remaining 3013 not shown) Planarity restraints: 3222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG c 2 " 0.076 2.00e-02 2.50e+03 6.44e-02 5.18e+01 pdb=" C7 NAG c 2 " -0.036 2.00e-02 2.50e+03 pdb=" C8 NAG c 2 " 0.063 2.00e-02 2.50e+03 pdb=" N2 NAG c 2 " -0.098 2.00e-02 2.50e+03 pdb=" O7 NAG c 2 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG r 1 " -0.074 2.00e-02 2.50e+03 6.15e-02 4.73e+01 pdb=" C7 NAG r 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG r 1 " -0.059 2.00e-02 2.50e+03 pdb=" N2 NAG r 1 " 0.094 2.00e-02 2.50e+03 pdb=" O7 NAG r 1 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 281 " -0.084 2.00e-02 2.50e+03 4.45e-02 3.97e+01 pdb=" CG TYR J 281 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR J 281 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR J 281 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR J 281 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR J 281 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR J 281 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR J 281 " -0.064 2.00e-02 2.50e+03 ... (remaining 3219 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1410 2.75 - 3.29: 18460 3.29 - 3.83: 30748 3.83 - 4.36: 42465 4.36 - 4.90: 67681 Nonbonded interactions: 160764 Sorted by model distance: nonbonded pdb=" OD2 ASP J 324 " pdb="CA CA J2000 " model vdw 2.218 2.510 nonbonded pdb=" OD2 ASP B 324 " pdb="CA CA B2000 " model vdw 2.239 2.510 nonbonded pdb=" O HIS G 347 " pdb="CA CA G 501 " model vdw 2.252 2.510 nonbonded pdb=" OD2 ASP H 324 " pdb="CA CA H2000 " model vdw 2.275 2.510 nonbonded pdb=" OD2 ASP G 324 " pdb="CA CA G 501 " model vdw 2.291 2.510 ... (remaining 160759 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' selection = chain '2' selection = chain '4' selection = chain '7' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'g' selection = chain 'i' selection = chain 'j' selection = chain 'l' selection = chain 'o' selection = chain 'q' selection = chain 'r' selection = chain 't' selection = chain 'w' } ncs_group { reference = chain '3' selection = chain 'c' selection = chain 'k' selection = chain 's' } ncs_group { reference = chain '5' selection = chain 'e' selection = chain 'm' selection = chain 'u' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'G' and (resid 82 through 469 or resid 501)) selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'I' } 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: 10.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 51.890 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 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 0.102 18993 Z= 1.037 Angle : 1.752 14.536 25929 Z= 1.116 Chirality : 0.094 0.601 3016 Planarity : 0.010 0.064 3198 Dihedral : 13.443 98.749 7897 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 0.31 Ramachandran Plot: Outliers : 0.58 % Allowed : 3.77 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2252 helix: -1.12 (0.70), residues: 24 sheet: 0.04 (0.16), residues: 925 loop : -0.70 (0.16), residues: 1303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.013 TRP B 458 HIS 0.046 0.007 HIS H 168 PHE 0.057 0.013 PHE G 205 TYR 0.084 0.013 TYR J 281 ARG 0.030 0.003 ARG H 288 Details of bonding type rmsd link_NAG-ASN : bond 0.01782 ( 24) link_NAG-ASN : angle 5.35011 ( 72) link_ALPHA1-6 : bond 0.01550 ( 8) link_ALPHA1-6 : angle 3.20270 ( 24) link_BETA1-4 : bond 0.01548 ( 28) link_BETA1-4 : angle 4.16160 ( 84) link_ALPHA1-2 : bond 0.00289 ( 4) link_ALPHA1-2 : angle 4.89940 ( 12) link_ALPHA1-3 : bond 0.01904 ( 8) link_ALPHA1-3 : angle 2.87221 ( 24) hydrogen bonds : bond 0.16151 ( 572) hydrogen bonds : angle 8.58427 ( 1518) link_BETA1-6 : bond 0.01223 ( 4) link_BETA1-6 : angle 3.27205 ( 12) SS BOND : bond 0.04676 ( 42) SS BOND : angle 2.40405 ( 84) covalent geometry : bond 0.01489 (18875) covalent geometry : angle 1.70803 (25617) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 297 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 ASP cc_start: 0.7815 (m-30) cc_final: 0.6939 (m-30) REVERT: F 11 LEU cc_start: 0.8017 (tp) cc_final: 0.7664 (tt) REVERT: F 75 ILE cc_start: 0.9128 (mt) cc_final: 0.8911 (mp) REVERT: F 79 GLN cc_start: 0.7499 (mm-40) cc_final: 0.7050 (mp10) REVERT: A 43 GLN cc_start: 0.8830 (tt0) cc_final: 0.8480 (mt0) REVERT: A 65 GLN cc_start: 0.8812 (tt0) cc_final: 0.8611 (tp-100) REVERT: D 42 GLN cc_start: 0.8890 (mt0) cc_final: 0.8662 (mt0) REVERT: D 75 ILE cc_start: 0.9472 (mt) cc_final: 0.9241 (tt) REVERT: C 23 LYS cc_start: 0.9259 (ttmt) cc_final: 0.8999 (tttp) REVERT: C 36 TRP cc_start: 0.9275 (m100) cc_final: 0.8952 (m100) REVERT: C 64 PHE cc_start: 0.8594 (m-80) cc_final: 0.8256 (m-10) REVERT: C 81 MET cc_start: 0.8256 (tmm) cc_final: 0.8035 (tmm) REVERT: C 90 ASP cc_start: 0.7477 (m-30) cc_final: 0.6935 (m-30) REVERT: C 93 VAL cc_start: 0.9147 (t) cc_final: 0.8892 (p) REVERT: C 102 ASP cc_start: 0.9066 (p0) cc_final: 0.8703 (p0) REVERT: I 4 MET cc_start: 0.8606 (mmm) cc_final: 0.7799 (mmm) REVERT: I 6 GLN cc_start: 0.8277 (tt0) cc_final: 0.7883 (tt0) REVERT: I 42 GLN cc_start: 0.7786 (mt0) cc_final: 0.7228 (mp10) REVERT: I 82 ASP cc_start: 0.7994 (m-30) cc_final: 0.7645 (m-30) REVERT: I 109 ARG cc_start: 0.6332 (ptm160) cc_final: 0.5263 (pmt-80) REVERT: H 141 ASN cc_start: 0.9366 (t0) cc_final: 0.8904 (p0) REVERT: B 400 ARG cc_start: 0.8908 (ptm-80) cc_final: 0.8671 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.3888 time to fit residues: 162.1658 Evaluate side-chains 182 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 2.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 114 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 130 optimal weight: 0.7980 chunk 203 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 GLN ** E 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 GLN D 6 GLN C 6 GLN I 92 ASN G 274 HIS G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS J 468 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.083055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.060110 restraints weight = 43658.512| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.86 r_work: 0.2842 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18993 Z= 0.151 Angle : 0.713 9.403 25929 Z= 0.372 Chirality : 0.048 0.327 3016 Planarity : 0.004 0.029 3198 Dihedral : 8.575 73.930 3998 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.29 % Favored : 96.54 % Rotamer: Outliers : 0.88 % Allowed : 6.03 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2252 helix: -0.82 (0.84), residues: 24 sheet: -0.01 (0.16), residues: 948 loop : -0.13 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 178 HIS 0.007 0.001 HIS J 468 PHE 0.016 0.002 PHE B 410 TYR 0.014 0.002 TYR F 49 ARG 0.006 0.001 ARG C 106 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 24) link_NAG-ASN : angle 2.97291 ( 72) link_ALPHA1-6 : bond 0.00704 ( 8) link_ALPHA1-6 : angle 1.32928 ( 24) link_BETA1-4 : bond 0.00467 ( 28) link_BETA1-4 : angle 2.03962 ( 84) link_ALPHA1-2 : bond 0.00718 ( 4) link_ALPHA1-2 : angle 1.96572 ( 12) link_ALPHA1-3 : bond 0.01045 ( 8) link_ALPHA1-3 : angle 1.77734 ( 24) hydrogen bonds : bond 0.05030 ( 572) hydrogen bonds : angle 7.28439 ( 1518) link_BETA1-6 : bond 0.00690 ( 4) link_BETA1-6 : angle 1.43330 ( 12) SS BOND : bond 0.00452 ( 42) SS BOND : angle 1.25327 ( 84) covalent geometry : bond 0.00313 (18875) covalent geometry : angle 0.68048 (25617) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 48 MET cc_start: 0.9078 (mtm) cc_final: 0.8874 (mtm) REVERT: E 67 ARG cc_start: 0.7521 (mtm-85) cc_final: 0.6175 (mtm110) REVERT: E 90 ASP cc_start: 0.7183 (m-30) cc_final: 0.6941 (m-30) REVERT: F 11 LEU cc_start: 0.8038 (tp) cc_final: 0.7779 (tt) REVERT: F 13 LEU cc_start: 0.8141 (mt) cc_final: 0.7278 (mt) REVERT: F 79 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7087 (mp10) REVERT: F 85 ILE cc_start: 0.8658 (mm) cc_final: 0.8414 (mm) REVERT: F 104 LYS cc_start: 0.8088 (tppt) cc_final: 0.7736 (tppt) REVERT: A 46 GLU cc_start: 0.8516 (tp30) cc_final: 0.8291 (tm-30) REVERT: A 77 THR cc_start: 0.7514 (OUTLIER) cc_final: 0.7248 (p) REVERT: A 81 MET cc_start: 0.8151 (tmm) cc_final: 0.7492 (ttp) REVERT: D 70 GLU cc_start: 0.8699 (tt0) cc_final: 0.8490 (tt0) REVERT: D 75 ILE cc_start: 0.9445 (mt) cc_final: 0.9167 (tt) REVERT: C 12 LYS cc_start: 0.8327 (mmtm) cc_final: 0.8109 (mmtm) REVERT: C 23 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8481 (tttm) REVERT: C 31 ASN cc_start: 0.8724 (t0) cc_final: 0.8473 (t0) REVERT: C 36 TRP cc_start: 0.9161 (m100) cc_final: 0.8805 (m100) REVERT: C 102 ASP cc_start: 0.9112 (p0) cc_final: 0.8724 (p0) REVERT: I 4 MET cc_start: 0.8379 (mmm) cc_final: 0.7822 (mmm) REVERT: I 11 LEU cc_start: 0.8793 (tp) cc_final: 0.8481 (tt) REVERT: I 42 GLN cc_start: 0.7482 (mt0) cc_final: 0.7136 (mt0) REVERT: I 101 GLN cc_start: 0.8673 (mm110) cc_final: 0.8433 (pm20) REVERT: I 109 ARG cc_start: 0.6422 (ptm160) cc_final: 0.5024 (pmt-80) REVERT: H 103 ASP cc_start: 0.8253 (p0) cc_final: 0.8017 (m-30) outliers start: 17 outliers final: 7 residues processed: 221 average time/residue: 0.4001 time to fit residues: 125.4033 Evaluate side-chains 185 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain H residue 230 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 122 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 210 optimal weight: 0.9990 chunk 179 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 32 GLN E 65 GLN ** E 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 120 GLN ** D 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN G 347 HIS G 468 HIS H 347 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS J 468 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.081085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058132 restraints weight = 43685.076| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 2.82 r_work: 0.2799 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 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 : 0.005 0.047 18993 Z= 0.208 Angle : 0.689 9.348 25929 Z= 0.351 Chirality : 0.048 0.286 3016 Planarity : 0.004 0.046 3198 Dihedral : 7.835 66.397 3998 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.33 % Favored : 96.49 % Rotamer: Outliers : 1.29 % Allowed : 8.66 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2252 helix: -0.52 (0.83), residues: 24 sheet: -0.16 (0.17), residues: 866 loop : -0.07 (0.16), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 178 HIS 0.006 0.001 HIS J 468 PHE 0.022 0.002 PHE C 64 TYR 0.020 0.002 TYR H 121 ARG 0.006 0.001 ARG I 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 24) link_NAG-ASN : angle 2.69564 ( 72) link_ALPHA1-6 : bond 0.00481 ( 8) link_ALPHA1-6 : angle 1.43718 ( 24) link_BETA1-4 : bond 0.00433 ( 28) link_BETA1-4 : angle 1.91803 ( 84) link_ALPHA1-2 : bond 0.00445 ( 4) link_ALPHA1-2 : angle 2.28472 ( 12) link_ALPHA1-3 : bond 0.00714 ( 8) link_ALPHA1-3 : angle 1.94327 ( 24) hydrogen bonds : bond 0.04667 ( 572) hydrogen bonds : angle 6.85772 ( 1518) link_BETA1-6 : bond 0.00402 ( 4) link_BETA1-6 : angle 1.91470 ( 12) SS BOND : bond 0.00339 ( 42) SS BOND : angle 1.40436 ( 84) covalent geometry : bond 0.00471 (18875) covalent geometry : angle 0.65703 (25617) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 65 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7988 (tm-30) REVERT: E 67 ARG cc_start: 0.7483 (mtm-85) cc_final: 0.6280 (mtm110) REVERT: F 17 GLU cc_start: 0.8410 (tt0) cc_final: 0.8194 (pt0) REVERT: F 77 SER cc_start: 0.8530 (t) cc_final: 0.8159 (p) REVERT: F 79 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7205 (mp10) REVERT: F 104 LYS cc_start: 0.8388 (tppt) cc_final: 0.8171 (tppt) REVERT: A 12 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7811 (mmmt) REVERT: A 23 LYS cc_start: 0.9031 (tttm) cc_final: 0.8665 (tttp) REVERT: A 46 GLU cc_start: 0.8753 (tp30) cc_final: 0.8385 (tm-30) REVERT: D 18 ARG cc_start: 0.8492 (ttp80) cc_final: 0.8290 (ttp80) REVERT: D 24 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8209 (ttm-80) REVERT: D 75 ILE cc_start: 0.9440 (mt) cc_final: 0.9202 (tt) REVERT: C 12 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8106 (mmtm) REVERT: C 23 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8447 (tttm) REVERT: C 65 GLN cc_start: 0.8682 (tp40) cc_final: 0.8054 (tm-30) REVERT: C 94 TYR cc_start: 0.8184 (m-10) cc_final: 0.7977 (m-10) REVERT: C 102 ASP cc_start: 0.9194 (p0) cc_final: 0.8823 (p0) REVERT: I 4 MET cc_start: 0.8368 (mmm) cc_final: 0.7869 (mmm) REVERT: I 42 GLN cc_start: 0.7641 (mt0) cc_final: 0.7335 (mt0) REVERT: I 101 GLN cc_start: 0.8661 (mm110) cc_final: 0.8372 (pm20) REVERT: I 104 LYS cc_start: 0.8734 (mtpp) cc_final: 0.8462 (mmtt) REVERT: I 109 ARG cc_start: 0.6395 (ptm160) cc_final: 0.4925 (pmt-80) outliers start: 25 outliers final: 16 residues processed: 205 average time/residue: 0.3987 time to fit residues: 116.3826 Evaluate side-chains 187 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 67 ARG Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 169 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN A 65 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.058483 restraints weight = 43723.983| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.74 r_work: 0.2809 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18993 Z= 0.183 Angle : 0.639 8.938 25929 Z= 0.324 Chirality : 0.046 0.261 3016 Planarity : 0.003 0.044 3198 Dihedral : 7.143 56.924 3998 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.06 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 9.59 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.17), residues: 2252 helix: -1.11 (0.78), residues: 28 sheet: -0.14 (0.15), residues: 974 loop : -0.05 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 178 HIS 0.010 0.001 HIS J 468 PHE 0.015 0.002 PHE G 410 TYR 0.017 0.001 TYR F 49 ARG 0.008 0.001 ARG E 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00379 ( 24) link_NAG-ASN : angle 2.45203 ( 72) link_ALPHA1-6 : bond 0.00544 ( 8) link_ALPHA1-6 : angle 1.40476 ( 24) link_BETA1-4 : bond 0.00390 ( 28) link_BETA1-4 : angle 1.70769 ( 84) link_ALPHA1-2 : bond 0.00492 ( 4) link_ALPHA1-2 : angle 2.30313 ( 12) link_ALPHA1-3 : bond 0.00751 ( 8) link_ALPHA1-3 : angle 1.86231 ( 24) hydrogen bonds : bond 0.04214 ( 572) hydrogen bonds : angle 6.63627 ( 1518) link_BETA1-6 : bond 0.00248 ( 4) link_BETA1-6 : angle 1.41653 ( 12) SS BOND : bond 0.00402 ( 42) SS BOND : angle 0.93188 ( 84) covalent geometry : bond 0.00409 (18875) covalent geometry : angle 0.61288 (25617) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 2.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 12 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7682 (mmtt) REVERT: E 46 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7947 (tt0) REVERT: E 65 GLN cc_start: 0.8416 (tp-100) cc_final: 0.7911 (tm-30) REVERT: E 67 ARG cc_start: 0.7462 (mtm-85) cc_final: 0.6385 (mtm110) REVERT: F 13 LEU cc_start: 0.8355 (mt) cc_final: 0.8071 (mt) REVERT: F 79 GLN cc_start: 0.7608 (mm-40) cc_final: 0.6998 (mp10) REVERT: A 12 LYS cc_start: 0.8115 (mmtt) cc_final: 0.7813 (mmmt) REVERT: A 46 GLU cc_start: 0.8782 (tp30) cc_final: 0.8273 (tm-30) REVERT: A 107 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8043 (m-30) REVERT: D 45 ARG cc_start: 0.8559 (ttm-80) cc_final: 0.7927 (ttp80) REVERT: C 12 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8200 (mmtm) REVERT: C 23 LYS cc_start: 0.8890 (ttmt) cc_final: 0.8479 (tttm) REVERT: C 65 GLN cc_start: 0.8648 (tp40) cc_final: 0.7982 (tm-30) REVERT: C 102 ASP cc_start: 0.9241 (p0) cc_final: 0.8814 (p0) REVERT: I 4 MET cc_start: 0.8370 (mmm) cc_final: 0.7981 (mmm) REVERT: I 11 LEU cc_start: 0.8852 (tp) cc_final: 0.8648 (tt) REVERT: I 13 LEU cc_start: 0.8384 (mt) cc_final: 0.8155 (mm) REVERT: I 42 GLN cc_start: 0.7654 (mt0) cc_final: 0.7342 (mt0) REVERT: I 101 GLN cc_start: 0.8632 (mm110) cc_final: 0.8323 (pm20) REVERT: I 109 ARG cc_start: 0.6369 (ptm160) cc_final: 0.4990 (pmt-80) REVERT: H 101 SER cc_start: 0.9464 (t) cc_final: 0.9129 (m) outliers start: 24 outliers final: 16 residues processed: 205 average time/residue: 0.5132 time to fit residues: 150.6829 Evaluate side-chains 190 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 2.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 35 SER Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 43 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 103 optimal weight: 0.0170 chunk 44 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 overall best weight: 2.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 GLN A 65 GLN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.078108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.056398 restraints weight = 43792.976| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.73 r_work: 0.2760 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 18993 Z= 0.300 Angle : 0.713 9.435 25929 Z= 0.359 Chirality : 0.049 0.266 3016 Planarity : 0.004 0.066 3198 Dihedral : 7.465 58.724 3998 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.14 % Rotamer: Outliers : 1.44 % Allowed : 10.06 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.17), residues: 2252 helix: 0.10 (0.89), residues: 24 sheet: -0.26 (0.16), residues: 953 loop : -0.18 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 178 HIS 0.009 0.001 HIS J 468 PHE 0.018 0.002 PHE H 410 TYR 0.017 0.002 TYR H 121 ARG 0.007 0.001 ARG A 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 24) link_NAG-ASN : angle 2.54412 ( 72) link_ALPHA1-6 : bond 0.00350 ( 8) link_ALPHA1-6 : angle 1.60291 ( 24) link_BETA1-4 : bond 0.00297 ( 28) link_BETA1-4 : angle 1.90739 ( 84) link_ALPHA1-2 : bond 0.00198 ( 4) link_ALPHA1-2 : angle 2.42736 ( 12) link_ALPHA1-3 : bond 0.00370 ( 8) link_ALPHA1-3 : angle 2.39984 ( 24) hydrogen bonds : bond 0.04764 ( 572) hydrogen bonds : angle 6.71966 ( 1518) link_BETA1-6 : bond 0.00215 ( 4) link_BETA1-6 : angle 1.59357 ( 12) SS BOND : bond 0.00578 ( 42) SS BOND : angle 1.22316 ( 84) covalent geometry : bond 0.00687 (18875) covalent geometry : angle 0.68395 (25617) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 1.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8466 (mp0) REVERT: E 65 GLN cc_start: 0.8466 (tp-100) cc_final: 0.7856 (tm-30) REVERT: E 67 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.6509 (mtm110) REVERT: F 61 ARG cc_start: 0.8084 (ptm-80) cc_final: 0.7131 (ptm-80) REVERT: F 104 LYS cc_start: 0.8233 (tppt) cc_final: 0.8026 (tppt) REVERT: F 105 VAL cc_start: 0.8846 (t) cc_final: 0.8583 (t) REVERT: F 106 GLU cc_start: 0.6667 (tp30) cc_final: 0.6457 (tp30) REVERT: A 12 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7961 (mmmt) REVERT: A 46 GLU cc_start: 0.8897 (tp30) cc_final: 0.8580 (tm-30) REVERT: D 45 ARG cc_start: 0.8578 (ttm-80) cc_final: 0.7969 (ttp80) REVERT: C 12 LYS cc_start: 0.8624 (mmtm) cc_final: 0.8414 (mmtm) REVERT: C 23 LYS cc_start: 0.8918 (ttmt) cc_final: 0.8478 (tttp) REVERT: C 65 GLN cc_start: 0.8828 (tp40) cc_final: 0.7959 (tm-30) REVERT: C 94 TYR cc_start: 0.8207 (m-10) cc_final: 0.7875 (m-10) REVERT: C 102 ASP cc_start: 0.9297 (p0) cc_final: 0.8907 (p0) REVERT: I 4 MET cc_start: 0.8437 (mmm) cc_final: 0.7999 (mmm) REVERT: I 11 LEU cc_start: 0.8837 (tp) cc_final: 0.8508 (tt) REVERT: I 42 GLN cc_start: 0.7799 (mt0) cc_final: 0.7506 (mt0) REVERT: I 47 LEU cc_start: 0.9062 (tp) cc_final: 0.8792 (tt) REVERT: I 54 ARG cc_start: 0.8573 (ttp-110) cc_final: 0.8223 (ttp-110) REVERT: I 101 GLN cc_start: 0.8594 (mm110) cc_final: 0.8349 (pm20) REVERT: I 109 ARG cc_start: 0.6186 (ptm160) cc_final: 0.4729 (pmt-80) REVERT: H 343 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7853 (mt-10) outliers start: 28 outliers final: 19 residues processed: 200 average time/residue: 0.4247 time to fit residues: 120.2531 Evaluate side-chains 188 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 362 MET Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 104 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 130 optimal weight: 0.5980 chunk 160 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 199 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.080984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058051 restraints weight = 43657.015| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.83 r_work: 0.2802 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18993 Z= 0.148 Angle : 0.629 9.387 25929 Z= 0.316 Chirality : 0.046 0.244 3016 Planarity : 0.003 0.033 3198 Dihedral : 6.897 59.243 3998 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.06 % Favored : 96.76 % Rotamer: Outliers : 1.19 % Allowed : 10.78 % Favored : 88.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.17), residues: 2252 helix: -0.87 (0.78), residues: 28 sheet: -0.15 (0.16), residues: 932 loop : -0.10 (0.17), residues: 1292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 178 HIS 0.009 0.001 HIS J 468 PHE 0.014 0.002 PHE H 410 TYR 0.017 0.001 TYR F 49 ARG 0.012 0.000 ARG F 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00235 ( 24) link_NAG-ASN : angle 2.26829 ( 72) link_ALPHA1-6 : bond 0.00569 ( 8) link_ALPHA1-6 : angle 1.41083 ( 24) link_BETA1-4 : bond 0.00390 ( 28) link_BETA1-4 : angle 1.54361 ( 84) link_ALPHA1-2 : bond 0.00484 ( 4) link_ALPHA1-2 : angle 2.45470 ( 12) link_ALPHA1-3 : bond 0.00848 ( 8) link_ALPHA1-3 : angle 1.74866 ( 24) hydrogen bonds : bond 0.03941 ( 572) hydrogen bonds : angle 6.47484 ( 1518) link_BETA1-6 : bond 0.00269 ( 4) link_BETA1-6 : angle 1.39929 ( 12) SS BOND : bond 0.00314 ( 42) SS BOND : angle 0.86115 ( 84) covalent geometry : bond 0.00327 (18875) covalent geometry : angle 0.60638 (25617) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 180 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 65 GLN cc_start: 0.8455 (tp-100) cc_final: 0.7830 (tm-30) REVERT: E 67 ARG cc_start: 0.7501 (mtm-85) cc_final: 0.6538 (mtm110) REVERT: F 4 MET cc_start: 0.8755 (mmm) cc_final: 0.8452 (mmm) REVERT: F 61 ARG cc_start: 0.7724 (ptm-80) cc_final: 0.7022 (ptm-80) REVERT: F 104 LYS cc_start: 0.8203 (tppt) cc_final: 0.7983 (tppt) REVERT: F 105 VAL cc_start: 0.8852 (t) cc_final: 0.8623 (t) REVERT: F 106 GLU cc_start: 0.6684 (tp30) cc_final: 0.6433 (tp30) REVERT: A 12 LYS cc_start: 0.8268 (mmtt) cc_final: 0.8044 (mmmt) REVERT: A 46 GLU cc_start: 0.8900 (tp30) cc_final: 0.8394 (tm-30) REVERT: D 45 ARG cc_start: 0.8558 (ttm-80) cc_final: 0.7959 (ttp80) REVERT: C 12 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8327 (mmtm) REVERT: C 23 LYS cc_start: 0.8898 (ttmt) cc_final: 0.8454 (tttp) REVERT: C 65 GLN cc_start: 0.8798 (tp40) cc_final: 0.7973 (tm-30) REVERT: C 94 TYR cc_start: 0.8101 (m-10) cc_final: 0.7755 (m-10) REVERT: C 102 ASP cc_start: 0.9276 (p0) cc_final: 0.8831 (p0) REVERT: I 4 MET cc_start: 0.8351 (mmm) cc_final: 0.7963 (mmm) REVERT: I 42 GLN cc_start: 0.7740 (mt0) cc_final: 0.7439 (mt0) REVERT: I 47 LEU cc_start: 0.9078 (tp) cc_final: 0.8852 (tt) REVERT: I 54 ARG cc_start: 0.8576 (ttp-110) cc_final: 0.8297 (ttp-110) REVERT: I 101 GLN cc_start: 0.8596 (mm110) cc_final: 0.8330 (pm20) REVERT: I 104 LYS cc_start: 0.8769 (mtpp) cc_final: 0.8501 (mmtt) REVERT: I 109 ARG cc_start: 0.6213 (ptm160) cc_final: 0.4810 (pmt-80) REVERT: H 101 SER cc_start: 0.9439 (t) cc_final: 0.9106 (m) outliers start: 23 outliers final: 18 residues processed: 197 average time/residue: 0.4037 time to fit residues: 112.0310 Evaluate side-chains 189 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 100 optimal weight: 5.9990 chunk 201 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 144 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 217 optimal weight: 0.6980 chunk 178 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN D 6 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.079404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.057326 restraints weight = 43786.337| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.78 r_work: 0.2777 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18993 Z= 0.237 Angle : 0.662 9.216 25929 Z= 0.331 Chirality : 0.047 0.246 3016 Planarity : 0.004 0.045 3198 Dihedral : 7.007 55.992 3998 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.09 % Favored : 95.74 % Rotamer: Outliers : 1.44 % Allowed : 10.99 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.17), residues: 2252 helix: -0.70 (0.82), residues: 28 sheet: -0.22 (0.16), residues: 953 loop : -0.13 (0.18), residues: 1271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 178 HIS 0.009 0.001 HIS J 468 PHE 0.017 0.002 PHE J 410 TYR 0.017 0.002 TYR F 49 ARG 0.007 0.001 ARG E 63 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 24) link_NAG-ASN : angle 2.34595 ( 72) link_ALPHA1-6 : bond 0.00451 ( 8) link_ALPHA1-6 : angle 1.50207 ( 24) link_BETA1-4 : bond 0.00302 ( 28) link_BETA1-4 : angle 1.69012 ( 84) link_ALPHA1-2 : bond 0.00324 ( 4) link_ALPHA1-2 : angle 2.35092 ( 12) link_ALPHA1-3 : bond 0.00545 ( 8) link_ALPHA1-3 : angle 2.10640 ( 24) hydrogen bonds : bond 0.04310 ( 572) hydrogen bonds : angle 6.50572 ( 1518) link_BETA1-6 : bond 0.00188 ( 4) link_BETA1-6 : angle 1.48444 ( 12) SS BOND : bond 0.00367 ( 42) SS BOND : angle 0.97055 ( 84) covalent geometry : bond 0.00545 (18875) covalent geometry : angle 0.63697 (25617) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8373 (mp0) REVERT: E 65 GLN cc_start: 0.8468 (tp-100) cc_final: 0.7764 (tm-30) REVERT: E 67 ARG cc_start: 0.7554 (mtm-85) cc_final: 0.6615 (mtm110) REVERT: F 4 MET cc_start: 0.8773 (mmm) cc_final: 0.8573 (mmm) REVERT: F 24 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8192 (mtm180) REVERT: F 61 ARG cc_start: 0.7779 (ptm-80) cc_final: 0.7049 (ptm-80) REVERT: F 104 LYS cc_start: 0.8265 (tppt) cc_final: 0.8020 (tppt) REVERT: F 105 VAL cc_start: 0.8884 (t) cc_final: 0.8637 (t) REVERT: F 106 GLU cc_start: 0.6781 (tp30) cc_final: 0.6516 (tp30) REVERT: A 12 LYS cc_start: 0.8333 (mmtt) cc_final: 0.7940 (mmmt) REVERT: A 46 GLU cc_start: 0.8903 (tp30) cc_final: 0.8380 (tm-30) REVERT: D 45 ARG cc_start: 0.8543 (ttm-80) cc_final: 0.8025 (ttp80) REVERT: C 12 LYS cc_start: 0.8609 (mmtm) cc_final: 0.8334 (mmtm) REVERT: C 23 LYS cc_start: 0.8907 (ttmt) cc_final: 0.8453 (tttp) REVERT: C 65 GLN cc_start: 0.8848 (tp40) cc_final: 0.8017 (tm-30) REVERT: C 94 TYR cc_start: 0.8146 (m-10) cc_final: 0.7784 (m-10) REVERT: C 102 ASP cc_start: 0.9275 (p0) cc_final: 0.8866 (p0) REVERT: I 4 MET cc_start: 0.8373 (mmm) cc_final: 0.7944 (mmm) REVERT: I 42 GLN cc_start: 0.7794 (mt0) cc_final: 0.7501 (mt0) REVERT: I 47 LEU cc_start: 0.9075 (tp) cc_final: 0.8856 (tt) REVERT: I 54 ARG cc_start: 0.8600 (ttp-110) cc_final: 0.8304 (ttp80) REVERT: I 101 GLN cc_start: 0.8564 (mm110) cc_final: 0.8317 (pm20) REVERT: I 109 ARG cc_start: 0.6243 (ptm160) cc_final: 0.4838 (pmt-80) outliers start: 28 outliers final: 21 residues processed: 196 average time/residue: 0.4251 time to fit residues: 118.3619 Evaluate side-chains 191 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 128 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.079876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058094 restraints weight = 43624.831| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.70 r_work: 0.2804 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18993 Z= 0.190 Angle : 0.649 12.697 25929 Z= 0.322 Chirality : 0.046 0.242 3016 Planarity : 0.003 0.038 3198 Dihedral : 6.820 50.975 3998 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.69 % Favored : 96.14 % Rotamer: Outliers : 1.39 % Allowed : 11.50 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2252 helix: -0.75 (0.80), residues: 28 sheet: -0.17 (0.16), residues: 945 loop : -0.14 (0.18), residues: 1279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 178 HIS 0.009 0.001 HIS J 468 PHE 0.015 0.002 PHE J 410 TYR 0.017 0.001 TYR F 49 ARG 0.008 0.000 ARG D 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 24) link_NAG-ASN : angle 2.25808 ( 72) link_ALPHA1-6 : bond 0.00501 ( 8) link_ALPHA1-6 : angle 1.47454 ( 24) link_BETA1-4 : bond 0.00330 ( 28) link_BETA1-4 : angle 1.58284 ( 84) link_ALPHA1-2 : bond 0.00381 ( 4) link_ALPHA1-2 : angle 2.38158 ( 12) link_ALPHA1-3 : bond 0.00682 ( 8) link_ALPHA1-3 : angle 1.95948 ( 24) hydrogen bonds : bond 0.04090 ( 572) hydrogen bonds : angle 6.41048 ( 1518) link_BETA1-6 : bond 0.00207 ( 4) link_BETA1-6 : angle 1.43479 ( 12) SS BOND : bond 0.00305 ( 42) SS BOND : angle 0.81245 ( 84) covalent geometry : bond 0.00429 (18875) covalent geometry : angle 0.62609 (25617) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 6.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8260 (mp0) REVERT: E 12 LYS cc_start: 0.8017 (mmtt) cc_final: 0.7466 (mmtt) REVERT: E 29 PHE cc_start: 0.5736 (OUTLIER) cc_final: 0.5190 (m-80) REVERT: E 65 GLN cc_start: 0.8437 (tp-100) cc_final: 0.7696 (tm-30) REVERT: E 67 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.6629 (mtm110) REVERT: F 24 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8236 (mtm180) REVERT: F 61 ARG cc_start: 0.7760 (ptm-80) cc_final: 0.7140 (ptm-80) REVERT: F 104 LYS cc_start: 0.8282 (tppt) cc_final: 0.8064 (tppt) REVERT: F 105 VAL cc_start: 0.8881 (t) cc_final: 0.8547 (t) REVERT: F 106 GLU cc_start: 0.6818 (tp30) cc_final: 0.6510 (tp30) REVERT: A 12 LYS cc_start: 0.8315 (mmtt) cc_final: 0.8001 (mmmt) REVERT: A 46 GLU cc_start: 0.8889 (tp30) cc_final: 0.8360 (tm-30) REVERT: A 111 GLU cc_start: 0.8294 (tt0) cc_final: 0.8094 (pm20) REVERT: D 24 ARG cc_start: 0.8297 (ttm-80) cc_final: 0.8013 (ttm-80) REVERT: D 45 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8010 (ttp80) REVERT: D 79 GLN cc_start: 0.8861 (mt0) cc_final: 0.8599 (mt0) REVERT: C 12 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8352 (mmtm) REVERT: C 23 LYS cc_start: 0.8903 (ttmt) cc_final: 0.8458 (tttp) REVERT: C 65 GLN cc_start: 0.8860 (tp40) cc_final: 0.8012 (tm-30) REVERT: C 94 TYR cc_start: 0.8103 (m-10) cc_final: 0.7744 (m-10) REVERT: C 102 ASP cc_start: 0.9263 (p0) cc_final: 0.8852 (p0) REVERT: I 4 MET cc_start: 0.8349 (mmm) cc_final: 0.7927 (mmm) REVERT: I 37 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.8075 (tp40) REVERT: I 42 GLN cc_start: 0.7767 (mt0) cc_final: 0.7482 (mt0) REVERT: I 47 LEU cc_start: 0.9110 (tp) cc_final: 0.8903 (tt) REVERT: I 54 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8328 (ttp80) REVERT: I 101 GLN cc_start: 0.8553 (mm110) cc_final: 0.8308 (pm20) REVERT: I 104 LYS cc_start: 0.8756 (mtpp) cc_final: 0.8500 (mmtt) REVERT: I 109 ARG cc_start: 0.6185 (ptm160) cc_final: 0.4893 (pmt-80) outliers start: 27 outliers final: 22 residues processed: 198 average time/residue: 0.5279 time to fit residues: 150.7113 Evaluate side-chains 197 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 221 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.080198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.057518 restraints weight = 44159.662| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.82 r_work: 0.2785 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 18993 Z= 0.199 Angle : 0.655 11.577 25929 Z= 0.325 Chirality : 0.046 0.242 3016 Planarity : 0.003 0.040 3198 Dihedral : 6.747 46.517 3998 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.17 % Favored : 95.65 % Rotamer: Outliers : 1.65 % Allowed : 11.40 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.17), residues: 2252 helix: -0.67 (0.81), residues: 28 sheet: -0.15 (0.16), residues: 929 loop : -0.12 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 178 HIS 0.010 0.001 HIS J 468 PHE 0.017 0.002 PHE C 29 TYR 0.017 0.001 TYR F 49 ARG 0.009 0.000 ARG D 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00331 ( 24) link_NAG-ASN : angle 2.24440 ( 72) link_ALPHA1-6 : bond 0.00483 ( 8) link_ALPHA1-6 : angle 1.49332 ( 24) link_BETA1-4 : bond 0.00311 ( 28) link_BETA1-4 : angle 1.57761 ( 84) link_ALPHA1-2 : bond 0.00349 ( 4) link_ALPHA1-2 : angle 2.34504 ( 12) link_ALPHA1-3 : bond 0.00629 ( 8) link_ALPHA1-3 : angle 2.00438 ( 24) hydrogen bonds : bond 0.04133 ( 572) hydrogen bonds : angle 6.39951 ( 1518) link_BETA1-6 : bond 0.00177 ( 4) link_BETA1-6 : angle 1.43374 ( 12) SS BOND : bond 0.00312 ( 42) SS BOND : angle 0.80037 ( 84) covalent geometry : bond 0.00451 (18875) covalent geometry : angle 0.63276 (25617) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 2.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8388 (mp0) REVERT: E 12 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7515 (mmtt) REVERT: E 29 PHE cc_start: 0.5806 (OUTLIER) cc_final: 0.5348 (m-80) REVERT: E 67 ARG cc_start: 0.7532 (mtm-85) cc_final: 0.6655 (mtm110) REVERT: F 24 ARG cc_start: 0.8539 (ttm-80) cc_final: 0.8299 (mtm180) REVERT: F 61 ARG cc_start: 0.7867 (ptm-80) cc_final: 0.7211 (ptm-80) REVERT: F 105 VAL cc_start: 0.8848 (t) cc_final: 0.8499 (t) REVERT: F 106 GLU cc_start: 0.6811 (tp30) cc_final: 0.6431 (tp30) REVERT: A 12 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8062 (mmmt) REVERT: A 46 GLU cc_start: 0.8898 (tp30) cc_final: 0.8381 (tm-30) REVERT: A 111 GLU cc_start: 0.8311 (tt0) cc_final: 0.8102 (pm20) REVERT: D 24 ARG cc_start: 0.8342 (ttm-80) cc_final: 0.8068 (ttm-80) REVERT: D 45 ARG cc_start: 0.8448 (ttm-80) cc_final: 0.7989 (ttp80) REVERT: C 12 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8372 (mmtm) REVERT: C 23 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8404 (tttp) REVERT: C 65 GLN cc_start: 0.8856 (tp40) cc_final: 0.8022 (tm-30) REVERT: C 94 TYR cc_start: 0.8087 (m-10) cc_final: 0.7716 (m-10) REVERT: C 102 ASP cc_start: 0.9273 (p0) cc_final: 0.8859 (p0) REVERT: I 4 MET cc_start: 0.8369 (mmm) cc_final: 0.7948 (mmm) REVERT: I 37 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8084 (tp40) REVERT: I 42 GLN cc_start: 0.7763 (mt0) cc_final: 0.7470 (mt0) REVERT: I 54 ARG cc_start: 0.8633 (ttp-110) cc_final: 0.8307 (ttp-110) REVERT: I 75 ILE cc_start: 0.9198 (mt) cc_final: 0.8967 (pt) REVERT: I 104 LYS cc_start: 0.8730 (mtpp) cc_final: 0.8480 (mmtt) REVERT: I 109 ARG cc_start: 0.6278 (ptm160) cc_final: 0.4950 (pmt-80) outliers start: 32 outliers final: 26 residues processed: 201 average time/residue: 0.4118 time to fit residues: 116.3675 Evaluate side-chains 199 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 48 ILE Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 215 VAL Chi-restraints excluded: chain J residue 230 CYS Chi-restraints excluded: chain J residue 245 ASN Chi-restraints excluded: chain J residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 30 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 126 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 135 optimal weight: 0.0970 chunk 220 optimal weight: 4.9990 chunk 1 optimal weight: 0.0060 chunk 143 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 441 ASN J 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.081833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.059739 restraints weight = 43765.169| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.80 r_work: 0.2844 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 18993 Z= 0.109 Angle : 0.623 11.543 25929 Z= 0.308 Chirality : 0.045 0.238 3016 Planarity : 0.003 0.061 3198 Dihedral : 6.147 43.600 3998 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.46 % Favored : 96.36 % Rotamer: Outliers : 1.19 % Allowed : 12.02 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2252 helix: -0.85 (0.76), residues: 28 sheet: -0.08 (0.17), residues: 872 loop : -0.13 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 178 HIS 0.010 0.001 HIS J 468 PHE 0.010 0.001 PHE J 410 TYR 0.016 0.001 TYR F 49 ARG 0.013 0.000 ARG D 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 24) link_NAG-ASN : angle 1.99890 ( 72) link_ALPHA1-6 : bond 0.00672 ( 8) link_ALPHA1-6 : angle 1.35002 ( 24) link_BETA1-4 : bond 0.00439 ( 28) link_BETA1-4 : angle 1.30831 ( 84) link_ALPHA1-2 : bond 0.00594 ( 4) link_ALPHA1-2 : angle 2.28415 ( 12) link_ALPHA1-3 : bond 0.01007 ( 8) link_ALPHA1-3 : angle 1.46766 ( 24) hydrogen bonds : bond 0.03491 ( 572) hydrogen bonds : angle 6.17446 ( 1518) link_BETA1-6 : bond 0.00248 ( 4) link_BETA1-6 : angle 1.27743 ( 12) SS BOND : bond 0.00181 ( 42) SS BOND : angle 0.58305 ( 84) covalent geometry : bond 0.00233 (18875) covalent geometry : angle 0.60698 (25617) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4504 Ramachandran restraints generated. 2252 Oldfield, 0 Emsley, 2252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 10 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8472 (mp0) REVERT: E 12 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7542 (mmtt) REVERT: E 29 PHE cc_start: 0.5815 (OUTLIER) cc_final: 0.5304 (m-80) REVERT: E 67 ARG cc_start: 0.7495 (mtm-85) cc_final: 0.6792 (mtm110) REVERT: F 24 ARG cc_start: 0.8485 (ttm-80) cc_final: 0.8285 (mtm180) REVERT: A 10 GLU cc_start: 0.7067 (mm-30) cc_final: 0.6853 (mp0) REVERT: A 12 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8134 (mmmt) REVERT: A 46 GLU cc_start: 0.8858 (tp30) cc_final: 0.8366 (tm-30) REVERT: D 24 ARG cc_start: 0.8296 (ttm-80) cc_final: 0.8094 (ttm-80) REVERT: D 45 ARG cc_start: 0.8421 (ttm-80) cc_final: 0.8019 (ttp80) REVERT: C 12 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8423 (mmtm) REVERT: C 23 LYS cc_start: 0.8895 (ttmt) cc_final: 0.8444 (tttm) REVERT: C 46 GLU cc_start: 0.8742 (tp30) cc_final: 0.8288 (tt0) REVERT: C 65 GLN cc_start: 0.8836 (tp40) cc_final: 0.8064 (tm-30) REVERT: C 93 VAL cc_start: 0.8944 (t) cc_final: 0.8621 (p) REVERT: C 94 TYR cc_start: 0.8008 (m-10) cc_final: 0.7648 (m-10) REVERT: C 102 ASP cc_start: 0.9245 (p0) cc_final: 0.8808 (p0) REVERT: I 4 MET cc_start: 0.8331 (mmm) cc_final: 0.7910 (mmm) REVERT: I 37 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7952 (tp-100) REVERT: I 42 GLN cc_start: 0.7709 (mt0) cc_final: 0.7469 (mt0) REVERT: I 54 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8330 (ttp-110) REVERT: I 75 ILE cc_start: 0.9201 (mt) cc_final: 0.8946 (pt) REVERT: I 104 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8421 (mmtt) REVERT: I 109 ARG cc_start: 0.6309 (ptm160) cc_final: 0.5023 (pmt-80) REVERT: H 101 SER cc_start: 0.9305 (t) cc_final: 0.9033 (m) outliers start: 23 outliers final: 18 residues processed: 206 average time/residue: 0.4002 time to fit residues: 116.7997 Evaluate side-chains 198 residues out of total 1939 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 29 PHE Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain G residue 230 CYS Chi-restraints excluded: chain G residue 242 THR Chi-restraints excluded: chain G residue 362 MET Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 230 CYS Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 230 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 221 optimal weight: 0.6980 chunk 140 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 195 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 168 optimal weight: 0.4980 chunk 28 optimal weight: 0.4980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 468 HIS ** H 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.080309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.059090 restraints weight = 43317.623| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.71 r_work: 0.2816 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18993 Z= 0.161 Angle : 0.643 11.011 25929 Z= 0.315 Chirality : 0.046 0.227 3016 Planarity : 0.003 0.045 3198 Dihedral : 6.229 42.731 3998 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.91 % Favored : 95.91 % Rotamer: Outliers : 1.39 % Allowed : 12.22 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.67 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.18), residues: 2252 helix: -0.52 (0.82), residues: 28 sheet: -0.03 (0.16), residues: 929 loop : -0.01 (0.18), residues: 1295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 178 HIS 0.010 0.001 HIS J 468 PHE 0.013 0.002 PHE J 410 TYR 0.017 0.001 TYR F 49 ARG 0.010 0.000 ARG D 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 24) link_NAG-ASN : angle 2.48620 ( 72) link_ALPHA1-6 : bond 0.00556 ( 8) link_ALPHA1-6 : angle 1.47148 ( 24) link_BETA1-4 : bond 0.00391 ( 28) link_BETA1-4 : angle 1.45142 ( 84) link_ALPHA1-2 : bond 0.00431 ( 4) link_ALPHA1-2 : angle 2.17760 ( 12) link_ALPHA1-3 : bond 0.00729 ( 8) link_ALPHA1-3 : angle 1.85452 ( 24) hydrogen bonds : bond 0.03846 ( 572) hydrogen bonds : angle 6.22996 ( 1518) link_BETA1-6 : bond 0.00196 ( 4) link_BETA1-6 : angle 1.41431 ( 12) SS BOND : bond 0.00266 ( 42) SS BOND : angle 0.71438 ( 84) covalent geometry : bond 0.00364 (18875) covalent geometry : angle 0.61939 (25617) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10425.14 seconds wall clock time: 182 minutes 53.61 seconds (10973.61 seconds total)