Starting phenix.real_space_refine on Mon Apr 28 13:32:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bpd_44772/04_2025/9bpd_44772.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bpd_44772/04_2025/9bpd_44772.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bpd_44772/04_2025/9bpd_44772.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bpd_44772/04_2025/9bpd_44772.map" model { file = "/net/cci-nas-00/data/ceres_data/9bpd_44772/04_2025/9bpd_44772.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bpd_44772/04_2025/9bpd_44772.cif" } resolution = 3.63 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= 0.002 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: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 54 5.16 5 C 4809 2.51 5 N 1248 2.21 5 O 1428 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 7551 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2415 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 15, 'TRANS': 290} Chain: "B" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2415 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 15, 'TRANS': 290} Chain: "C" Number of atoms: 2415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2415 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 15, 'TRANS': 290} 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: 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: "F" 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: "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: "H" 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: "A" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 46 Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.96, per 1000 atoms: 0.92 Number of scatterers: 7551 At special positions: 0 Unit cell: (88.536, 87.482, 111.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 9 15.00 Mg 3 11.99 O 1428 8.00 N 1248 7.00 C 4809 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 102 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 251 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 148 " distance=2.04 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 132 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 242 " - pdb=" SG CYS B 251 " distance=2.03 Simple disulfide: pdb=" SG CYS C 102 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 111 " - pdb=" SG CYS C 132 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 208 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 251 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 401 " - " ASN A 285 " " NAG B 401 " - " ASN B 285 " " NAG C 402 " - " ASN C 285 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 189 " " NAG F 1 " - " ASN B 165 " " NAG G 1 " - " ASN B 189 " " NAG H 1 " - " ASN C 165 " " NAG I 1 " - " ASN C 189 " Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.0 seconds 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1692 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 18 sheets defined 27.9% alpha, 45.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 21 through 34 removed outlier: 3.520A pdb=" N VAL A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 76 removed outlier: 3.609A pdb=" N TYR A 75 " --> pdb=" O ASP A 71 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 76' Processing helix chain 'A' and resid 106 through 110 removed outlier: 3.944A pdb=" N ARG A 110 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 118 removed outlier: 3.687A pdb=" N GLN A 116 " --> pdb=" O SER A 113 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY A 118 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 165 removed outlier: 3.871A pdb=" N GLU A 164 " --> pdb=" O MET A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 197 removed outlier: 4.202A pdb=" N THR A 197 " --> pdb=" O ALA A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.657A pdb=" N LEU A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.687A pdb=" N CYS A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 313 through 326 removed outlier: 4.154A pdb=" N ILE A 317 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 34 removed outlier: 3.749A pdb=" N LEU B 27 " --> pdb=" O ARG B 23 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE B 30 " --> pdb=" O GLN B 26 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR B 32 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 76 removed outlier: 3.608A pdb=" N TYR B 75 " --> pdb=" O ASP B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 removed outlier: 3.942A pdb=" N ARG B 110 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.688A pdb=" N GLN B 116 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 removed outlier: 3.870A pdb=" N GLU B 164 " --> pdb=" O MET B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 197 removed outlier: 4.202A pdb=" N THR B 197 " --> pdb=" O ALA B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 221 Processing helix chain 'B' and resid 223 through 231 removed outlier: 3.657A pdb=" N LEU B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 251 removed outlier: 3.688A pdb=" N CYS B 251 " --> pdb=" O TRP B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 264 Processing helix chain 'B' and resid 313 through 326 removed outlier: 4.153A pdb=" N ILE B 317 " --> pdb=" O ILE B 313 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 318 " --> pdb=" O ILE B 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 34 removed outlier: 3.749A pdb=" N LEU C 27 " --> pdb=" O ARG C 23 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 30 " --> pdb=" O GLN C 26 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE C 33 " --> pdb=" O ILE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 removed outlier: 3.609A pdb=" N TYR C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 110 removed outlier: 3.943A pdb=" N ARG C 110 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 118 removed outlier: 3.688A pdb=" N GLN C 116 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY C 118 " --> pdb=" O SER C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 165 removed outlier: 3.870A pdb=" N GLU C 164 " --> pdb=" O MET C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 197 removed outlier: 4.201A pdb=" N THR C 197 " --> pdb=" O ALA C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 221 Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.657A pdb=" N LEU C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 251 removed outlier: 3.687A pdb=" N CYS C 251 " --> pdb=" O TRP C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 264 Processing helix chain 'C' and resid 313 through 326 removed outlier: 4.154A pdb=" N ILE C 317 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 318 " --> pdb=" O ILE C 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 59 Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 65 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 97 removed outlier: 6.815A pdb=" N PHE A 296 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET A 91 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS A 294 " --> pdb=" O MET A 91 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL A 93 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 292 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU A 95 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ARG A 290 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLN A 97 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLU A 288 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 97 removed outlier: 6.815A pdb=" N PHE A 296 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET A 91 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS A 294 " --> pdb=" O MET A 91 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL A 93 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 292 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU A 95 " --> pdb=" O ARG A 290 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ARG A 290 " --> pdb=" O GLU A 95 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLN A 97 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLU A 288 " --> pdb=" O GLN A 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 99 through 102 removed outlier: 5.032A pdb=" N ARG A 131 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N GLN A 145 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR A 129 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N TRP A 147 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ILE A 127 " --> pdb=" O TRP A 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 59 Processing sheet with id=AA8, first strand: chain 'B' and resid 52 through 59 Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 65 Processing sheet with id=AB1, first strand: chain 'B' and resid 84 through 97 removed outlier: 6.816A pdb=" N PHE B 296 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET B 91 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS B 294 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL B 93 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 292 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU B 95 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ARG B 290 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLN B 97 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLU B 288 " --> pdb=" O GLN B 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 84 through 97 removed outlier: 6.816A pdb=" N PHE B 296 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET B 91 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LYS B 294 " --> pdb=" O MET B 91 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL B 93 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU B 292 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N GLU B 95 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ARG B 290 " --> pdb=" O GLU B 95 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLN B 97 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLU B 288 " --> pdb=" O GLN B 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 99 through 102 removed outlier: 5.032A pdb=" N ARG B 131 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N GLN B 145 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR B 129 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 9.333A pdb=" N TRP B 147 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ILE B 127 " --> pdb=" O TRP B 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 52 through 59 Processing sheet with id=AB5, first strand: chain 'C' and resid 52 through 59 Processing sheet with id=AB6, first strand: chain 'C' and resid 63 through 65 Processing sheet with id=AB7, first strand: chain 'C' and resid 84 through 97 removed outlier: 6.815A pdb=" N PHE C 296 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET C 91 " --> pdb=" O LYS C 294 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS C 294 " --> pdb=" O MET C 91 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL C 93 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 292 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU C 95 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ARG C 290 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLN C 97 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLU C 288 " --> pdb=" O GLN C 97 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 97 removed outlier: 6.815A pdb=" N PHE C 296 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N MET C 91 " --> pdb=" O LYS C 294 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LYS C 294 " --> pdb=" O MET C 91 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL C 93 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU C 292 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLU C 95 " --> pdb=" O ARG C 290 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ARG C 290 " --> pdb=" O GLU C 95 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLN C 97 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLU C 288 " --> pdb=" O GLN C 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 99 through 102 removed outlier: 5.032A pdb=" N ARG C 131 " --> pdb=" O GLU C 143 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N GLN C 145 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR C 129 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N TRP C 147 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N ILE C 127 " --> pdb=" O TRP C 147 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 753 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: 2.02 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2352 1.34 - 1.46: 1952 1.46 - 1.59: 3334 1.59 - 1.71: 12 1.71 - 1.83: 78 Bond restraints: 7728 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.54e+00 ... (remaining 7723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 9590 1.03 - 2.06: 690 2.06 - 3.10: 136 3.10 - 4.13: 39 4.13 - 5.16: 27 Bond angle restraints: 10482 Sorted by residual: angle pdb=" N ASP C 203 " pdb=" CA ASP C 203 " pdb=" C ASP C 203 " ideal model delta sigma weight residual 114.62 109.96 4.66 1.14e+00 7.69e-01 1.67e+01 angle pdb=" N ASP A 203 " pdb=" CA ASP A 203 " pdb=" C ASP A 203 " ideal model delta sigma weight residual 114.62 109.98 4.64 1.14e+00 7.69e-01 1.66e+01 angle pdb=" N ASP B 203 " pdb=" CA ASP B 203 " pdb=" C ASP B 203 " ideal model delta sigma weight residual 114.62 109.99 4.63 1.14e+00 7.69e-01 1.65e+01 angle pdb=" CA ASP B 203 " pdb=" C ASP B 203 " pdb=" N LYS B 204 " ideal model delta sigma weight residual 119.71 116.31 3.40 1.17e+00 7.31e-01 8.43e+00 angle pdb=" CA ASP C 203 " pdb=" C ASP C 203 " pdb=" N LYS C 204 " ideal model delta sigma weight residual 119.71 116.34 3.37 1.17e+00 7.31e-01 8.27e+00 ... (remaining 10477 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 4086 18.04 - 36.07: 561 36.07 - 54.11: 177 54.11 - 72.14: 18 72.14 - 90.18: 27 Dihedral angle restraints: 4869 sinusoidal: 2226 harmonic: 2643 Sorted by residual: dihedral pdb=" CB CYS C 117 " pdb=" SG CYS C 117 " pdb=" SG CYS C 142 " pdb=" CB CYS C 142 " ideal model delta sinusoidal sigma weight residual 93.00 -176.82 -90.18 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 -176.83 -90.17 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS B 117 " pdb=" SG CYS B 117 " pdb=" SG CYS B 142 " pdb=" CB CYS B 142 " ideal model delta sinusoidal sigma weight residual 93.00 -176.86 -90.14 1 1.00e+01 1.00e-02 9.62e+01 ... (remaining 4866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1023 0.071 - 0.141: 153 0.141 - 0.212: 3 0.212 - 0.282: 3 0.282 - 0.353: 6 Chirality restraints: 1188 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 1185 not shown) Planarity restraints: 1314 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 205 " -0.045 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO B 206 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 206 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 206 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 205 " 0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO C 206 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO C 206 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 206 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 205 " 0.045 5.00e-02 4.00e+02 6.78e-02 7.36e+00 pdb=" N PRO A 206 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " 0.038 5.00e-02 4.00e+02 ... (remaining 1311 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 111 2.62 - 3.19: 6498 3.19 - 3.76: 11174 3.76 - 4.33: 15124 4.33 - 4.90: 24877 Nonbonded interactions: 57784 Sorted by model distance: nonbonded pdb="MG MG A 402 " pdb=" O3B ATP C 401 " model vdw 2.046 2.170 nonbonded pdb=" O3B ATP B 403 " pdb="MG MG C 403 " model vdw 2.047 2.170 nonbonded pdb=" O3B ATP A 403 " pdb="MG MG B 402 " model vdw 2.047 2.170 nonbonded pdb=" O3G ATP A 403 " pdb="MG MG B 402 " model vdw 2.100 2.170 nonbonded pdb=" O3G ATP B 403 " pdb="MG MG C 403 " model vdw 2.100 2.170 ... (remaining 57779 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 21 through 326) selection = (chain 'B' and resid 21 through 326) selection = (chain 'C' and resid 21 through 326) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.090 Set scattering table: 0.150 Process input model: 26.870 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 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 : 0.003 0.032 7758 Z= 0.170 Angle : 0.683 7.232 10557 Z= 0.360 Chirality : 0.054 0.353 1188 Planarity : 0.004 0.068 1305 Dihedral : 17.660 86.216 3132 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.95 % Favored : 87.72 % Rotamer: Outliers : 0.38 % Allowed : 33.58 % Favored : 66.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.62 (0.26), residues: 912 helix: -1.28 (0.37), residues: 195 sheet: -0.06 (0.31), residues: 264 loop : -3.12 (0.23), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 240 HIS 0.002 0.001 HIS C 201 PHE 0.015 0.001 PHE A 166 TYR 0.019 0.001 TYR C 75 ARG 0.002 0.000 ARG C 199 Details of bonding type rmsd link_NAG-ASN : bond 0.01211 ( 9) link_NAG-ASN : angle 2.62826 ( 27) link_BETA1-4 : bond 0.00617 ( 6) link_BETA1-4 : angle 3.78410 ( 18) hydrogen bonds : bond 0.19105 ( 251) hydrogen bonds : angle 8.01670 ( 753) SS BOND : bond 0.00247 ( 15) SS BOND : angle 1.46109 ( 30) covalent geometry : bond 0.00344 ( 7728) covalent geometry : angle 0.64933 (10482) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 113 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7823 (ttt) cc_final: 0.7530 (ttm) REVERT: A 201 HIS cc_start: 0.6467 (t-90) cc_final: 0.6064 (t70) REVERT: A 283 MET cc_start: 0.8631 (mmm) cc_final: 0.8322 (mmm) REVERT: C 98 MET cc_start: 0.7688 (ttt) cc_final: 0.7462 (ttm) REVERT: C 201 HIS cc_start: 0.6676 (t-90) cc_final: 0.6390 (t-170) REVERT: C 283 MET cc_start: 0.8765 (mmm) cc_final: 0.8428 (mmt) outliers start: 3 outliers final: 0 residues processed: 116 average time/residue: 0.1876 time to fit residues: 30.2510 Evaluate side-chains 107 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN ** A 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 GLN ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 HIS C 97 GLN ** C 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.168473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.113106 restraints weight = 10968.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117748 restraints weight = 6104.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.120592 restraints weight = 4427.513| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7758 Z= 0.188 Angle : 0.663 6.991 10557 Z= 0.340 Chirality : 0.054 0.309 1188 Planarity : 0.004 0.044 1305 Dihedral : 9.222 58.557 1419 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 11.29 % Favored : 88.38 % Rotamer: Outliers : 2.89 % Allowed : 28.81 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.54 (0.26), residues: 912 helix: -1.64 (0.34), residues: 213 sheet: 0.00 (0.30), residues: 294 loop : -3.08 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 240 HIS 0.004 0.001 HIS B 201 PHE 0.032 0.002 PHE C 166 TYR 0.015 0.002 TYR A 289 ARG 0.002 0.000 ARG B 259 Details of bonding type rmsd link_NAG-ASN : bond 0.00833 ( 9) link_NAG-ASN : angle 2.81342 ( 27) link_BETA1-4 : bond 0.00272 ( 6) link_BETA1-4 : angle 2.02152 ( 18) hydrogen bonds : bond 0.03574 ( 251) hydrogen bonds : angle 5.14365 ( 753) SS BOND : bond 0.00236 ( 15) SS BOND : angle 1.33748 ( 30) covalent geometry : bond 0.00440 ( 7728) covalent geometry : angle 0.64050 (10482) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8100 (ttt) cc_final: 0.7805 (ttm) REVERT: A 109 TYR cc_start: 0.7119 (m-80) cc_final: 0.6340 (m-80) REVERT: A 201 HIS cc_start: 0.7251 (t-90) cc_final: 0.6656 (t70) REVERT: C 75 TYR cc_start: 0.9031 (p90) cc_final: 0.8711 (p90) outliers start: 23 outliers final: 9 residues processed: 136 average time/residue: 0.1874 time to fit residues: 35.0284 Evaluate side-chains 115 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 141 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 79 optimal weight: 0.9990 chunk 29 optimal weight: 0.0170 chunk 74 optimal weight: 2.9990 chunk 84 optimal weight: 0.0020 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 89 optimal weight: 0.0020 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN B 99 GLN C 99 GLN C 201 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.172113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.115568 restraints weight = 11009.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.120336 restraints weight = 6126.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123348 restraints weight = 4454.393| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7758 Z= 0.120 Angle : 0.627 8.503 10557 Z= 0.314 Chirality : 0.052 0.290 1188 Planarity : 0.004 0.065 1305 Dihedral : 9.082 56.505 1419 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.29 % Favored : 88.49 % Rotamer: Outliers : 2.77 % Allowed : 28.30 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.29 (0.27), residues: 912 helix: -1.30 (0.36), residues: 213 sheet: 0.26 (0.30), residues: 294 loop : -3.10 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 36 HIS 0.004 0.001 HIS C 40 PHE 0.031 0.001 PHE B 166 TYR 0.024 0.001 TYR C 289 ARG 0.004 0.000 ARG C 121 Details of bonding type rmsd link_NAG-ASN : bond 0.00885 ( 9) link_NAG-ASN : angle 2.69887 ( 27) link_BETA1-4 : bond 0.00483 ( 6) link_BETA1-4 : angle 2.10142 ( 18) hydrogen bonds : bond 0.03173 ( 251) hydrogen bonds : angle 4.77122 ( 753) SS BOND : bond 0.00222 ( 15) SS BOND : angle 1.16934 ( 30) covalent geometry : bond 0.00269 ( 7728) covalent geometry : angle 0.60521 (10482) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8044 (ttt) cc_final: 0.7742 (ttm) REVERT: A 201 HIS cc_start: 0.7205 (t-90) cc_final: 0.6536 (t70) REVERT: B 75 TYR cc_start: 0.8994 (p90) cc_final: 0.8719 (p90) REVERT: B 109 TYR cc_start: 0.6757 (m-80) cc_final: 0.5705 (m-80) REVERT: B 250 GLN cc_start: 0.8331 (mt0) cc_final: 0.7865 (mt0) REVERT: C 75 TYR cc_start: 0.9012 (p90) cc_final: 0.8701 (p90) outliers start: 22 outliers final: 11 residues processed: 141 average time/residue: 0.1845 time to fit residues: 35.8112 Evaluate side-chains 120 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 167 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 30.0000 chunk 18 optimal weight: 0.0020 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.171465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.114759 restraints weight = 11037.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119536 restraints weight = 6136.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122541 restraints weight = 4465.059| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7758 Z= 0.133 Angle : 0.637 7.838 10557 Z= 0.318 Chirality : 0.052 0.295 1188 Planarity : 0.004 0.054 1305 Dihedral : 8.936 56.923 1419 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 3.77 % Allowed : 27.80 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.22 (0.27), residues: 912 helix: -1.20 (0.36), residues: 213 sheet: 0.30 (0.30), residues: 294 loop : -3.08 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 36 HIS 0.002 0.001 HIS C 201 PHE 0.030 0.001 PHE B 166 TYR 0.016 0.001 TYR B 289 ARG 0.010 0.000 ARG A 121 Details of bonding type rmsd link_NAG-ASN : bond 0.00787 ( 9) link_NAG-ASN : angle 2.67738 ( 27) link_BETA1-4 : bond 0.00456 ( 6) link_BETA1-4 : angle 2.09921 ( 18) hydrogen bonds : bond 0.03046 ( 251) hydrogen bonds : angle 4.60095 ( 753) SS BOND : bond 0.00199 ( 15) SS BOND : angle 1.11070 ( 30) covalent geometry : bond 0.00307 ( 7728) covalent geometry : angle 0.61547 (10482) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7481 (mt) REVERT: A 201 HIS cc_start: 0.7198 (t-90) cc_final: 0.6455 (t70) REVERT: A 293 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8398 (mt) REVERT: B 250 GLN cc_start: 0.8344 (mt0) cc_final: 0.7872 (mp10) REVERT: C 28 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7599 (mt) outliers start: 30 outliers final: 13 residues processed: 142 average time/residue: 0.1814 time to fit residues: 35.6031 Evaluate side-chains 123 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 167 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 73 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 18 optimal weight: 0.0060 chunk 40 optimal weight: 0.0070 chunk 82 optimal weight: 0.0570 chunk 35 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 overall best weight: 0.2932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.173585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.117038 restraints weight = 10996.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.121876 restraints weight = 6119.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.124878 restraints weight = 4458.572| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7758 Z= 0.112 Angle : 0.609 6.112 10557 Z= 0.305 Chirality : 0.051 0.284 1188 Planarity : 0.003 0.028 1305 Dihedral : 8.658 55.338 1419 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 2.77 % Allowed : 28.30 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.16 (0.27), residues: 912 helix: -1.07 (0.38), residues: 213 sheet: 0.34 (0.30), residues: 294 loop : -3.11 (0.26), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 36 HIS 0.003 0.001 HIS A 40 PHE 0.028 0.001 PHE B 166 TYR 0.015 0.001 TYR B 289 ARG 0.006 0.000 ARG B 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00830 ( 9) link_NAG-ASN : angle 2.55263 ( 27) link_BETA1-4 : bond 0.00481 ( 6) link_BETA1-4 : angle 2.04922 ( 18) hydrogen bonds : bond 0.02955 ( 251) hydrogen bonds : angle 4.47448 ( 753) SS BOND : bond 0.00197 ( 15) SS BOND : angle 1.02453 ( 30) covalent geometry : bond 0.00251 ( 7728) covalent geometry : angle 0.58840 (10482) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7466 (mt) REVERT: A 143 GLU cc_start: 0.7635 (tp30) cc_final: 0.7431 (tp30) REVERT: A 201 HIS cc_start: 0.7268 (t-90) cc_final: 0.6640 (t70) REVERT: A 293 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8303 (mt) outliers start: 22 outliers final: 15 residues processed: 131 average time/residue: 0.1579 time to fit residues: 29.5801 Evaluate side-chains 128 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 167 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 62 optimal weight: 0.0770 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.0370 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.172613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117675 restraints weight = 11000.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122512 restraints weight = 5952.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.125568 restraints weight = 4274.180| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7758 Z= 0.121 Angle : 0.609 6.686 10557 Z= 0.305 Chirality : 0.051 0.289 1188 Planarity : 0.003 0.023 1305 Dihedral : 8.522 56.370 1419 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 3.14 % Allowed : 28.68 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.13 (0.28), residues: 912 helix: -1.08 (0.37), residues: 213 sheet: 0.38 (0.31), residues: 294 loop : -3.09 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 36 HIS 0.001 0.000 HIS B 201 PHE 0.028 0.001 PHE B 166 TYR 0.030 0.001 TYR B 289 ARG 0.004 0.000 ARG B 23 Details of bonding type rmsd link_NAG-ASN : bond 0.00731 ( 9) link_NAG-ASN : angle 2.59277 ( 27) link_BETA1-4 : bond 0.00453 ( 6) link_BETA1-4 : angle 2.03162 ( 18) hydrogen bonds : bond 0.02890 ( 251) hydrogen bonds : angle 4.37646 ( 753) SS BOND : bond 0.00189 ( 15) SS BOND : angle 1.01168 ( 30) covalent geometry : bond 0.00275 ( 7728) covalent geometry : angle 0.58804 (10482) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7434 (mt) REVERT: A 98 MET cc_start: 0.7924 (ttt) cc_final: 0.7697 (ttm) REVERT: A 201 HIS cc_start: 0.7326 (t-90) cc_final: 0.6681 (t70) REVERT: A 293 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8327 (mt) REVERT: C 28 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7642 (mt) REVERT: C 288 GLU cc_start: 0.8585 (pm20) cc_final: 0.8230 (pt0) outliers start: 25 outliers final: 17 residues processed: 138 average time/residue: 0.1731 time to fit residues: 33.5892 Evaluate side-chains 125 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 191 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 89 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 56 optimal weight: 0.3980 chunk 87 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.171846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.115268 restraints weight = 10996.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120083 restraints weight = 6116.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.123007 restraints weight = 4451.365| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7758 Z= 0.132 Angle : 0.629 6.819 10557 Z= 0.315 Chirality : 0.052 0.287 1188 Planarity : 0.003 0.031 1305 Dihedral : 8.460 57.210 1419 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 3.14 % Allowed : 28.68 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.16 (0.28), residues: 912 helix: -1.10 (0.37), residues: 213 sheet: 0.33 (0.31), residues: 294 loop : -3.08 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 36 HIS 0.001 0.000 HIS C 201 PHE 0.029 0.001 PHE C 166 TYR 0.020 0.001 TYR B 289 ARG 0.011 0.000 ARG A 121 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 9) link_NAG-ASN : angle 2.59325 ( 27) link_BETA1-4 : bond 0.00441 ( 6) link_BETA1-4 : angle 2.00707 ( 18) hydrogen bonds : bond 0.02919 ( 251) hydrogen bonds : angle 4.35937 ( 753) SS BOND : bond 0.00186 ( 15) SS BOND : angle 0.98572 ( 30) covalent geometry : bond 0.00304 ( 7728) covalent geometry : angle 0.60970 (10482) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.034 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: A 28 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7472 (mt) REVERT: A 98 MET cc_start: 0.7934 (ttt) cc_final: 0.7690 (ttm) REVERT: A 201 HIS cc_start: 0.7362 (t-90) cc_final: 0.7068 (t-170) REVERT: A 293 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8357 (mt) REVERT: C 28 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7647 (mt) outliers start: 25 outliers final: 18 residues processed: 132 average time/residue: 0.1609 time to fit residues: 30.5606 Evaluate side-chains 125 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 191 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 60 optimal weight: 30.0000 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 28 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 30.0000 chunk 5 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.171326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.114546 restraints weight = 11137.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119372 restraints weight = 6150.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122392 restraints weight = 4460.205| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7758 Z= 0.133 Angle : 0.629 6.977 10557 Z= 0.316 Chirality : 0.052 0.283 1188 Planarity : 0.003 0.033 1305 Dihedral : 8.401 57.505 1419 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 2.77 % Allowed : 29.18 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.17 (0.28), residues: 912 helix: -1.08 (0.37), residues: 213 sheet: 0.29 (0.31), residues: 294 loop : -3.07 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 36 HIS 0.002 0.000 HIS B 201 PHE 0.029 0.001 PHE B 166 TYR 0.016 0.001 TYR B 289 ARG 0.005 0.000 ARG A 121 Details of bonding type rmsd link_NAG-ASN : bond 0.00682 ( 9) link_NAG-ASN : angle 2.56334 ( 27) link_BETA1-4 : bond 0.00428 ( 6) link_BETA1-4 : angle 1.97628 ( 18) hydrogen bonds : bond 0.02894 ( 251) hydrogen bonds : angle 4.31976 ( 753) SS BOND : bond 0.00186 ( 15) SS BOND : angle 0.99561 ( 30) covalent geometry : bond 0.00306 ( 7728) covalent geometry : angle 0.60981 (10482) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7468 (mt) REVERT: A 98 MET cc_start: 0.7942 (ttt) cc_final: 0.7696 (ttm) REVERT: A 201 HIS cc_start: 0.7409 (t-90) cc_final: 0.7079 (t-170) REVERT: A 250 GLN cc_start: 0.8381 (mt0) cc_final: 0.7920 (mt0) REVERT: B 270 SER cc_start: 0.8349 (OUTLIER) cc_final: 0.8090 (p) REVERT: C 28 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7526 (mt) REVERT: C 250 GLN cc_start: 0.8316 (mt0) cc_final: 0.7931 (mt0) REVERT: C 270 SER cc_start: 0.8354 (OUTLIER) cc_final: 0.8020 (p) REVERT: C 288 GLU cc_start: 0.8517 (pm20) cc_final: 0.8115 (pt0) outliers start: 22 outliers final: 17 residues processed: 122 average time/residue: 0.1710 time to fit residues: 29.6920 Evaluate side-chains 120 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 270 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 15 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 71 optimal weight: 0.0000 chunk 87 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 30 optimal weight: 30.0000 chunk 79 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.164156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.108684 restraints weight = 11164.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113082 restraints weight = 6271.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115759 restraints weight = 4606.227| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7758 Z= 0.237 Angle : 0.719 7.962 10557 Z= 0.364 Chirality : 0.056 0.320 1188 Planarity : 0.004 0.035 1305 Dihedral : 8.791 56.999 1419 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.84 % Favored : 88.16 % Rotamer: Outliers : 3.65 % Allowed : 28.55 % Favored : 67.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.38 (0.27), residues: 912 helix: -1.49 (0.34), residues: 213 sheet: 0.56 (0.32), residues: 276 loop : -3.25 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 36 HIS 0.002 0.001 HIS B 201 PHE 0.044 0.002 PHE C 166 TYR 0.015 0.002 TYR B 281 ARG 0.005 0.001 ARG A 121 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 9) link_NAG-ASN : angle 2.97974 ( 27) link_BETA1-4 : bond 0.00351 ( 6) link_BETA1-4 : angle 2.14067 ( 18) hydrogen bonds : bond 0.03455 ( 251) hydrogen bonds : angle 4.72609 ( 753) SS BOND : bond 0.00248 ( 15) SS BOND : angle 1.26612 ( 30) covalent geometry : bond 0.00550 ( 7728) covalent geometry : angle 0.69683 (10482) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8056 (ttt) cc_final: 0.7804 (ttm) REVERT: A 270 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8173 (p) REVERT: B 270 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8310 (p) REVERT: C 28 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7541 (mt) REVERT: C 270 SER cc_start: 0.8574 (OUTLIER) cc_final: 0.8089 (p) outliers start: 29 outliers final: 23 residues processed: 114 average time/residue: 0.1855 time to fit residues: 30.1325 Evaluate side-chains 116 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 270 SER Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 161 MET Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 3 optimal weight: 3.9990 chunk 77 optimal weight: 0.0470 chunk 7 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.166542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.111207 restraints weight = 10957.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.115689 restraints weight = 6000.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118654 restraints weight = 4370.427| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7758 Z= 0.157 Angle : 0.664 7.019 10557 Z= 0.336 Chirality : 0.053 0.296 1188 Planarity : 0.003 0.026 1305 Dihedral : 8.777 59.933 1419 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.22 % Allowed : 10.75 % Favored : 89.04 % Rotamer: Outliers : 2.89 % Allowed : 28.68 % Favored : 68.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.32 (0.27), residues: 912 helix: -1.35 (0.36), residues: 213 sheet: 0.34 (0.31), residues: 288 loop : -3.15 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 36 HIS 0.002 0.001 HIS B 201 PHE 0.037 0.002 PHE C 166 TYR 0.013 0.001 TYR C 75 ARG 0.008 0.000 ARG A 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 9) link_NAG-ASN : angle 2.76641 ( 27) link_BETA1-4 : bond 0.00445 ( 6) link_BETA1-4 : angle 1.92486 ( 18) hydrogen bonds : bond 0.03071 ( 251) hydrogen bonds : angle 4.47758 ( 753) SS BOND : bond 0.00229 ( 15) SS BOND : angle 1.30525 ( 30) covalent geometry : bond 0.00363 ( 7728) covalent geometry : angle 0.64256 (10482) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1824 Ramachandran restraints generated. 912 Oldfield, 0 Emsley, 912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8048 (ttt) cc_final: 0.7786 (ttm) REVERT: B 270 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8267 (p) REVERT: C 28 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7537 (mt) REVERT: C 270 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8053 (p) outliers start: 23 outliers final: 18 residues processed: 115 average time/residue: 0.1710 time to fit residues: 27.9317 Evaluate side-chains 111 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 69 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 102 CYS Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 291 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 31 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 73 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.167963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109789 restraints weight = 11194.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.114699 restraints weight = 6017.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.117662 restraints weight = 4365.352| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7758 Z= 0.162 Angle : 0.678 6.882 10557 Z= 0.343 Chirality : 0.053 0.296 1188 Planarity : 0.004 0.034 1305 Dihedral : 8.768 59.884 1419 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.62 % Favored : 88.38 % Rotamer: Outliers : 2.77 % Allowed : 29.06 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -2.33 (0.27), residues: 912 helix: -1.33 (0.36), residues: 213 sheet: 0.29 (0.31), residues: 288 loop : -3.14 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 36 HIS 0.001 0.000 HIS B 201 PHE 0.038 0.002 PHE B 166 TYR 0.012 0.001 TYR C 75 ARG 0.007 0.000 ARG A 199 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 9) link_NAG-ASN : angle 2.77559 ( 27) link_BETA1-4 : bond 0.00401 ( 6) link_BETA1-4 : angle 1.93534 ( 18) hydrogen bonds : bond 0.03027 ( 251) hydrogen bonds : angle 4.50262 ( 753) SS BOND : bond 0.00276 ( 15) SS BOND : angle 1.52677 ( 30) covalent geometry : bond 0.00378 ( 7728) covalent geometry : angle 0.65583 (10482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2794.70 seconds wall clock time: 49 minutes 0.73 seconds (2940.73 seconds total)