Starting phenix.real_space_refine on Fri Mar 6 10:50:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u5s_20654/03_2026/6u5s_20654_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u5s_20654/03_2026/6u5s_20654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u5s_20654/03_2026/6u5s_20654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u5s_20654/03_2026/6u5s_20654.map" model { file = "/net/cci-nas-00/data/ceres_data/6u5s_20654/03_2026/6u5s_20654_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u5s_20654/03_2026/6u5s_20654_trim.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10724 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 36 5.16 5 C 7473 2.51 5 N 1949 2.21 5 O 2248 1.98 5 H 9755 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21461 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 5176 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 365} Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 10, 'ASP:plan': 6, 'ASN:plan1': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 115 Chain: "B" Number of atoms: 5357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 5357 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 365} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 Chain: "C" Number of atoms: 5292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 5292 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 365} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 125 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 9, 'ASP:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 93 Chain: "D" Number of atoms: 5368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 5368 Classifications: {'peptide': 376} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 365} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 90 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 9, 'ASP:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 73 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.46, per 1000 atoms: 0.21 Number of scatterers: 21461 At special positions: 0 Unit cell: (148.174, 128.986, 84.214, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 O 2248 8.00 N 1949 7.00 C 7473 6.00 H 9755 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 315 " distance=2.03 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 315 " 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " NAG-ASN " NAG E 1 " - " ASN A 355 " " NAG F 1 " - " ASN A 241 " " NAG G 1 " - " ASN B 355 " " NAG H 1 " - " ASN B 241 " " NAG I 1 " - " ASN C 355 " " NAG J 1 " - " ASN C 241 " " NAG K 1 " - " ASN D 355 " " NAG L 1 " - " ASN D 241 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 743.9 milliseconds 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2784 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 18 sheets defined 40.2% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 22 through 36 Processing helix chain 'A' and resid 54 through 68 Processing helix chain 'A' and resid 81 through 93 Processing helix chain 'A' and resid 117 through 128 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.639A pdb=" N GLU A 185 " --> pdb=" O PHE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.691A pdb=" N THR A 264 " --> pdb=" O GLU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 301 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.843A pdb=" N VAL A 327 " --> pdb=" O TRP A 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 81 through 93 Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 143 through 157 removed outlier: 4.262A pdb=" N GLU B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 4.128A pdb=" N LEU B 186 " --> pdb=" O GLN B 182 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.559A pdb=" N THR B 264 " --> pdb=" O GLU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 324 through 335 removed outlier: 4.213A pdb=" N GLU B 328 " --> pdb=" O GLY B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 36 Processing helix chain 'C' and resid 54 through 68 Processing helix chain 'C' and resid 81 through 93 Processing helix chain 'C' and resid 117 through 128 Processing helix chain 'C' and resid 143 through 155 Processing helix chain 'C' and resid 172 through 185 removed outlier: 3.639A pdb=" N GLU C 185 " --> pdb=" O PHE C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.690A pdb=" N THR C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 301 Processing helix chain 'C' and resid 323 through 334 removed outlier: 3.843A pdb=" N VAL C 327 " --> pdb=" O TRP C 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 143 through 157 removed outlier: 4.263A pdb=" N GLU D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 187 removed outlier: 4.128A pdb=" N LEU D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.559A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 324 through 335 removed outlier: 4.213A pdb=" N GLU D 328 " --> pdb=" O GLY D 324 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 47 removed outlier: 5.853A pdb=" N ILE A 12 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N HIS A 46 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE A 14 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N ALA A 72 " --> pdb=" O SER A 11 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 164 removed outlier: 6.419A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 222 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE A 360 " --> pdb=" O ILE A 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 337 through 339 removed outlier: 3.568A pdb=" N VAL A 338 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 13 Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.233A pdb=" N GLY B 16 " --> pdb=" O ASP B 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA7, first strand: chain 'B' and resid 162 through 164 removed outlier: 6.617A pdb=" N LEU B 136 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.485A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY B 372 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLU B 362 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LYS B 370 " --> pdb=" O GLU B 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 337 through 339 removed outlier: 4.134A pdb=" N LYS B 346 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 42 through 47 removed outlier: 5.855A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 162 through 164 removed outlier: 6.419A pdb=" N LEU C 136 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 222 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE C 360 " --> pdb=" O ILE C 371 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 337 through 339 removed outlier: 3.568A pdb=" N VAL C 338 " --> pdb=" O ILE C 345 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS C 346 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 13 Processing sheet with id=AB5, first strand: chain 'D' and resid 47 through 49 removed outlier: 6.234A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 97 through 98 Processing sheet with id=AB7, first strand: chain 'D' and resid 162 through 164 removed outlier: 6.617A pdb=" N LEU D 136 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.485A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY D 372 " --> pdb=" O ILE D 360 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 337 through 339 removed outlier: 4.134A pdb=" N LYS D 346 " --> pdb=" O ILE D 354 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1482 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: 4.90 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9747 1.03 - 1.22: 8 1.22 - 1.42: 5089 1.42 - 1.61: 6809 1.61 - 1.81: 56 Bond restraints: 21709 Sorted by residual: bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.65e+00 bond pdb=" C5 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.28e+00 ... (remaining 21704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.65: 38396 7.65 - 15.30: 0 15.30 - 22.95: 2 22.95 - 30.60: 4 30.60 - 38.24: 12 Bond angle restraints: 38414 Sorted by residual: angle pdb=" N ASP C 171 " pdb=" CA ASP C 171 " pdb=" HA ASP C 171 " ideal model delta sigma weight residual 110.00 71.76 38.24 3.00e+00 1.11e-01 1.63e+02 angle pdb=" CB GLU C 305 " pdb=" CA GLU C 305 " pdb=" HA GLU C 305 " ideal model delta sigma weight residual 109.00 71.36 37.64 3.00e+00 1.11e-01 1.57e+02 angle pdb=" C LYS B 172 " pdb=" CA LYS B 172 " pdb=" HA LYS B 172 " ideal model delta sigma weight residual 109.00 72.25 36.75 3.00e+00 1.11e-01 1.50e+02 angle pdb=" CB GLU B 175 " pdb=" CA GLU B 175 " pdb=" HA GLU B 175 " ideal model delta sigma weight residual 109.00 72.66 36.34 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C GLU C 305 " pdb=" CA GLU C 305 " pdb=" HA GLU C 305 " ideal model delta sigma weight residual 109.00 73.00 36.00 3.00e+00 1.11e-01 1.44e+02 ... (remaining 38409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 10277 21.78 - 43.57: 447 43.57 - 65.35: 161 65.35 - 87.13: 44 87.13 - 108.92: 24 Dihedral angle restraints: 10953 sinusoidal: 5757 harmonic: 5196 Sorted by residual: dihedral pdb=" CB CYS B 63 " pdb=" SG CYS B 63 " pdb=" SG CYS B 315 " pdb=" CB CYS B 315 " ideal model delta sinusoidal sigma weight residual -86.00 -131.10 45.10 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS D 63 " pdb=" SG CYS D 63 " pdb=" SG CYS D 315 " pdb=" CB CYS D 315 " ideal model delta sinusoidal sigma weight residual -86.00 -131.05 45.05 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS A 63 " pdb=" SG CYS A 63 " pdb=" SG CYS A 315 " pdb=" CB CYS A 315 " ideal model delta sinusoidal sigma weight residual -86.00 -125.01 39.01 1 1.00e+01 1.00e-02 2.14e+01 ... (remaining 10950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.276: 1907 0.276 - 0.552: 4 0.552 - 0.828: 0 0.828 - 1.104: 4 1.104 - 1.381: 2 Chirality restraints: 1917 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.76e+03 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.02 -1.38 2.00e-02 2.50e+03 4.75e+03 chirality pdb=" C1 NAG J 2 " pdb=" O4 NAG J 1 " pdb=" C2 NAG J 2 " pdb=" O5 NAG J 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-02 2.50e+03 2.24e+03 ... (remaining 1914 not shown) Planarity restraints: 3529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO A 99 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO C 99 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO D 99 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " -0.018 5.00e-02 4.00e+02 ... (remaining 3526 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.16: 678 2.16 - 2.77: 39546 2.77 - 3.38: 56499 3.38 - 3.99: 73741 3.99 - 4.60: 116923 Nonbonded interactions: 287387 Sorted by model distance: nonbonded pdb=" H GLU C 305 " pdb=" HA GLU C 305 " model vdw 1.549 1.816 nonbonded pdb=" H LYS B 172 " pdb=" HA LYS B 172 " model vdw 1.561 1.816 nonbonded pdb=" HH TYR B 77 " pdb=" O PHE B 101 " model vdw 1.634 2.450 nonbonded pdb=" HH TYR D 77 " pdb=" O PHE D 101 " model vdw 1.635 2.450 nonbonded pdb=" H ASP C 171 " pdb=" HA ASP C 171 " model vdw 1.642 1.816 ... (remaining 287382 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 10 through 140 or (resid 141 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name H or name HA )) or resid 142 through 233 or (resid 234 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 235 through 385)) selection = (chain 'B' and (resid 10 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 39 through 43 or (resid \ 44 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 45 through 46 or (resid 47 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 48 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 96 \ through 103 or (resid 104 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 105 or (resid 106 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 107 through 142 or (r \ esid 143 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD1 or name CD2 or name H or name HA )) or resid 144 or (resid 145 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 146 \ through 150 or (resid 151 through 152 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 153 through 169 or (resid 170 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 171 through 172 or (resid 173 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 174 through 177 or (resid 178 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 179 \ through 188 or (resid 189 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 190 through 194 or (resid 195 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 196 throug \ h 197 or (resid 198 through 200 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 201 through 206 or (resid 207 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 208 \ or (resid 209 through 210 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 211 through 278 or (resid 279 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name CE or name NZ \ or name H or name HA )) or resid 280 through 300 or (resid 301 through 303 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 304 through 345 or (resid 346 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 347 through 368 or (resid 369 through 37 \ 0 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 371 through 385)) selection = (chain 'C' and (resid 10 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 39 through 43 or (resid \ 44 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 45 through 46 or (resid 47 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 48 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 96 \ through 103 or (resid 104 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 105 or (resid 106 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 107 through 115 or (r \ esid 116 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 117 through 140 or (resid 141 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or n \ ame NH2 or name H or name HA )) or resid 142 or (resid 143 and (name N or name C \ A or name C or name O or name CB or name CG or name CD1 or name CD2 or name H or \ name HA )) or resid 144 or (resid 145 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 146 through 150 or (resid 151 thro \ ugh 152 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 153 through 169 or (resid 170 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 171 through 188 or (resid 18 \ 9 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 190 through 194 or (resid 195 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 196 through 198 or (resid 199 thro \ ugh 200 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 201 through 208 or (resid 209 through 210 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 211 through 233 \ or (resid 234 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 235 through 385)) selection = (chain 'D' and (resid 10 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 39 through 43 or (resid \ 44 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 45 through 46 or (resid 47 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 48 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 96 \ through 103 or (resid 104 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 105 or (resid 106 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 107 through 140 or (r \ esid 141 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2 or name H or name HA )) or re \ sid 142 or (resid 143 and (name N or name CA or name C or name O or name CB or n \ ame CG or name CD1 or name CD2 or name H or name HA )) or resid 144 or (resid 14 \ 5 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 146 through 150 or (resid 151 through 152 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 153 through 169 or (re \ sid 170 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 171 through 172 or (resid 173 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 174 through 177 or (resid 17 \ 8 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 179 through 188 or (resid 189 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 190 through 194 or (resid 195 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 196 through 197 or (resid 198 through 200 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 201 through 206 or (resid 20 \ 7 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 208 or (resid 209 through 210 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 211 through 233 or (resid 234 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 235 through 300 or (resid 301 through 303 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 304 through 351 or (resid 35 \ 2 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name CE or name NZ or name H or name HA )) or resid 353 through 368 or (resid 3 \ 69 through 370 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 371 through 385)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.120 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.400 Find NCS groups from input model: 0.320 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.004 0.066 11978 Z= 0.197 Angle : 0.922 35.641 16340 Z= 0.370 Chirality : 0.076 1.381 1917 Planarity : 0.002 0.038 2069 Dihedral : 16.033 108.919 4432 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.19), residues: 1496 helix: -0.51 (0.20), residues: 584 sheet: -3.42 (0.29), residues: 228 loop : -3.15 (0.20), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 30 TYR 0.008 0.001 TYR A 77 PHE 0.007 0.001 PHE A 76 TRP 0.011 0.001 TRP A 323 HIS 0.004 0.001 HIS D 219 Details of bonding type rmsd covalent geometry : bond 0.00374 (11954) covalent geometry : angle 0.48843 (16272) SS BOND : bond 0.00059 ( 4) SS BOND : angle 0.59509 ( 8) hydrogen bonds : bond 0.12534 ( 500) hydrogen bonds : angle 6.30743 ( 1482) link_BETA1-4 : bond 0.06490 ( 12) link_BETA1-4 : angle 16.60217 ( 36) link_NAG-ASN : bond 0.00227 ( 8) link_NAG-ASN : angle 1.70029 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.588 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 267 GLU cc_start: 0.8112 (tt0) cc_final: 0.7834 (tt0) REVERT: B 170 ASN cc_start: 0.7934 (m-40) cc_final: 0.7655 (m-40) REVERT: B 362 GLU cc_start: 0.8333 (mt-10) cc_final: 0.8084 (mt-10) REVERT: D 170 ASN cc_start: 0.7914 (m-40) cc_final: 0.7581 (m-40) REVERT: D 294 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7391 (tp30) REVERT: D 362 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8050 (mt-10) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2074 time to fit residues: 39.1580 Evaluate side-chains 59 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.0050 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 ASN A 60 ASN A 147 GLN A 290 GLN C 10 ASN C 60 ASN C 219 HIS C 290 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.097510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.078063 restraints weight = 66828.195| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.32 r_work: 0.3124 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11978 Z= 0.166 Angle : 0.534 6.631 16340 Z= 0.266 Chirality : 0.046 0.381 1917 Planarity : 0.003 0.037 2069 Dihedral : 11.173 92.708 2034 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.34 % Allowed : 5.24 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.21), residues: 1496 helix: 0.52 (0.21), residues: 616 sheet: -2.82 (0.29), residues: 248 loop : -2.57 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 331 TYR 0.016 0.001 TYR D 77 PHE 0.012 0.001 PHE A 41 TRP 0.009 0.001 TRP C 323 HIS 0.007 0.001 HIS C 219 Details of bonding type rmsd covalent geometry : bond 0.00371 (11954) covalent geometry : angle 0.51353 (16272) SS BOND : bond 0.00056 ( 4) SS BOND : angle 0.64168 ( 8) hydrogen bonds : bond 0.03548 ( 500) hydrogen bonds : angle 4.50859 ( 1482) link_BETA1-4 : bond 0.00704 ( 12) link_BETA1-4 : angle 2.85338 ( 36) link_NAG-ASN : bond 0.00477 ( 8) link_NAG-ASN : angle 1.79237 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 62 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASN cc_start: 0.8340 (m-40) cc_final: 0.7991 (m-40) REVERT: D 170 ASN cc_start: 0.8301 (m-40) cc_final: 0.7907 (m-40) outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 0.1563 time to fit residues: 16.1073 Evaluate side-chains 49 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain C residue 10 ASN Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 84 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 134 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 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 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.095931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.076420 restraints weight = 66600.613| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.31 r_work: 0.3086 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11978 Z= 0.169 Angle : 0.499 7.043 16340 Z= 0.251 Chirality : 0.045 0.371 1917 Planarity : 0.003 0.048 2069 Dihedral : 9.643 84.802 2034 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.34 % Allowed : 7.39 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.22), residues: 1496 helix: 0.86 (0.21), residues: 620 sheet: -2.46 (0.30), residues: 248 loop : -2.40 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 190 TYR 0.012 0.001 TYR B 77 PHE 0.008 0.001 PHE C 296 TRP 0.009 0.001 TRP C 323 HIS 0.006 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00378 (11954) covalent geometry : angle 0.47491 (16272) SS BOND : bond 0.00068 ( 4) SS BOND : angle 0.55345 ( 8) hydrogen bonds : bond 0.03581 ( 500) hydrogen bonds : angle 4.30512 ( 1482) link_BETA1-4 : bond 0.00405 ( 12) link_BETA1-4 : angle 2.59824 ( 36) link_NAG-ASN : bond 0.00653 ( 8) link_NAG-ASN : angle 2.46626 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASN cc_start: 0.8313 (m-40) cc_final: 0.7990 (m-40) REVERT: D 170 ASN cc_start: 0.8292 (m-40) cc_final: 0.7794 (m-40) outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.1568 time to fit residues: 13.1840 Evaluate side-chains 46 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain C residue 50 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 4 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.094114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.074558 restraints weight = 67369.409| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 3.31 r_work: 0.3042 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11978 Z= 0.166 Angle : 0.489 7.747 16340 Z= 0.249 Chirality : 0.045 0.376 1917 Planarity : 0.003 0.034 2069 Dihedral : 7.598 64.802 2034 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.52 % Allowed : 8.08 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.22), residues: 1496 helix: 1.28 (0.22), residues: 616 sheet: -2.16 (0.32), residues: 248 loop : -2.16 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.013 0.001 TYR B 77 PHE 0.007 0.001 PHE B 296 TRP 0.013 0.001 TRP C 323 HIS 0.009 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00374 (11954) covalent geometry : angle 0.46827 (16272) SS BOND : bond 0.00149 ( 4) SS BOND : angle 0.45858 ( 8) hydrogen bonds : bond 0.03412 ( 500) hydrogen bonds : angle 4.11863 ( 1482) link_BETA1-4 : bond 0.00449 ( 12) link_BETA1-4 : angle 2.12977 ( 36) link_NAG-ASN : bond 0.00502 ( 8) link_NAG-ASN : angle 2.68344 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 361 MET cc_start: 0.8447 (mtt) cc_final: 0.8007 (mtp) REVERT: B 170 ASN cc_start: 0.8355 (m-40) cc_final: 0.8042 (m-40) REVERT: D 170 ASN cc_start: 0.8225 (m-40) cc_final: 0.7840 (m-40) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 0.1675 time to fit residues: 13.9296 Evaluate side-chains 47 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 10 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 0.0270 chunk 45 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 137 optimal weight: 0.6980 chunk 144 optimal weight: 0.8980 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.094824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.075233 restraints weight = 66479.177| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 3.30 r_work: 0.3057 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11978 Z= 0.104 Angle : 0.450 8.031 16340 Z= 0.228 Chirality : 0.043 0.373 1917 Planarity : 0.003 0.033 2069 Dihedral : 7.019 57.715 2034 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.43 % Allowed : 9.02 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.22), residues: 1496 helix: 1.44 (0.22), residues: 620 sheet: -2.02 (0.32), residues: 248 loop : -1.98 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 300 TYR 0.009 0.001 TYR B 286 PHE 0.007 0.001 PHE C 296 TRP 0.009 0.001 TRP D 323 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00233 (11954) covalent geometry : angle 0.43362 (16272) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.41722 ( 8) hydrogen bonds : bond 0.03202 ( 500) hydrogen bonds : angle 3.97588 ( 1482) link_BETA1-4 : bond 0.00372 ( 12) link_BETA1-4 : angle 1.92349 ( 36) link_NAG-ASN : bond 0.00321 ( 8) link_NAG-ASN : angle 2.17602 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASN cc_start: 0.8318 (m-40) cc_final: 0.8005 (m-40) REVERT: D 170 ASN cc_start: 0.8195 (m-40) cc_final: 0.7812 (m-40) outliers start: 5 outliers final: 5 residues processed: 55 average time/residue: 0.1832 time to fit residues: 16.3548 Evaluate side-chains 51 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 236 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 142 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.094548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.074928 restraints weight = 67052.160| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.32 r_work: 0.3047 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11978 Z= 0.119 Angle : 0.444 7.722 16340 Z= 0.227 Chirality : 0.043 0.375 1917 Planarity : 0.003 0.034 2069 Dihedral : 6.165 58.961 2034 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.43 % Allowed : 9.11 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.23), residues: 1496 helix: 1.58 (0.22), residues: 620 sheet: -1.96 (0.32), residues: 248 loop : -1.82 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 190 TYR 0.010 0.001 TYR D 286 PHE 0.011 0.001 PHE A 181 TRP 0.010 0.001 TRP C 323 HIS 0.004 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00269 (11954) covalent geometry : angle 0.42795 (16272) SS BOND : bond 0.00130 ( 4) SS BOND : angle 0.40812 ( 8) hydrogen bonds : bond 0.03145 ( 500) hydrogen bonds : angle 3.90067 ( 1482) link_BETA1-4 : bond 0.00447 ( 12) link_BETA1-4 : angle 1.89995 ( 36) link_NAG-ASN : bond 0.00340 ( 8) link_NAG-ASN : angle 2.10306 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASN cc_start: 0.8320 (m-40) cc_final: 0.8022 (m-40) REVERT: D 170 ASN cc_start: 0.8170 (m-40) cc_final: 0.7826 (m-40) REVERT: D 362 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8384 (mt-10) outliers start: 5 outliers final: 4 residues processed: 59 average time/residue: 0.1577 time to fit residues: 15.9095 Evaluate side-chains 53 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 180 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 140 optimal weight: 3.9990 chunk 63 optimal weight: 0.0770 chunk 114 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** 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 = 0.3527 r_free = 0.3527 target = 0.094649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.075077 restraints weight = 66899.748| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.31 r_work: 0.3048 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11978 Z= 0.110 Angle : 0.433 7.021 16340 Z= 0.222 Chirality : 0.043 0.373 1917 Planarity : 0.003 0.035 2069 Dihedral : 5.590 59.193 2034 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.43 % Allowed : 9.54 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.23), residues: 1496 helix: 1.71 (0.22), residues: 616 sheet: -1.82 (0.33), residues: 248 loop : -1.62 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 190 TYR 0.009 0.001 TYR B 286 PHE 0.006 0.001 PHE A 296 TRP 0.010 0.001 TRP D 323 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00248 (11954) covalent geometry : angle 0.41798 (16272) SS BOND : bond 0.00119 ( 4) SS BOND : angle 0.39718 ( 8) hydrogen bonds : bond 0.03088 ( 500) hydrogen bonds : angle 3.84253 ( 1482) link_BETA1-4 : bond 0.00384 ( 12) link_BETA1-4 : angle 1.80505 ( 36) link_NAG-ASN : bond 0.00327 ( 8) link_NAG-ASN : angle 2.06643 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 ASN cc_start: 0.8330 (m-40) cc_final: 0.8037 (m-40) REVERT: D 170 ASN cc_start: 0.8176 (m-40) cc_final: 0.7826 (m-40) outliers start: 5 outliers final: 3 residues processed: 55 average time/residue: 0.1551 time to fit residues: 14.7424 Evaluate side-chains 52 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 180 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 31 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 52 optimal weight: 0.0070 chunk 106 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** 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 = 0.3516 r_free = 0.3516 target = 0.094103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.074388 restraints weight = 67381.369| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 3.32 r_work: 0.3036 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11978 Z= 0.133 Angle : 0.437 5.893 16340 Z= 0.226 Chirality : 0.043 0.375 1917 Planarity : 0.003 0.039 2069 Dihedral : 5.233 58.727 2034 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.43 % Allowed : 10.22 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.23), residues: 1496 helix: 1.68 (0.22), residues: 620 sheet: -1.81 (0.33), residues: 248 loop : -1.56 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 190 TYR 0.011 0.001 TYR C 77 PHE 0.007 0.001 PHE A 181 TRP 0.011 0.001 TRP D 323 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00302 (11954) covalent geometry : angle 0.42143 (16272) SS BOND : bond 0.00080 ( 4) SS BOND : angle 0.42194 ( 8) hydrogen bonds : bond 0.03168 ( 500) hydrogen bonds : angle 3.84468 ( 1482) link_BETA1-4 : bond 0.00406 ( 12) link_BETA1-4 : angle 1.79590 ( 36) link_NAG-ASN : bond 0.00361 ( 8) link_NAG-ASN : angle 2.10425 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 328 GLU cc_start: 0.7904 (tp30) cc_final: 0.7500 (tp30) REVERT: B 170 ASN cc_start: 0.8350 (m-40) cc_final: 0.8062 (m-40) REVERT: D 170 ASN cc_start: 0.8220 (m-40) cc_final: 0.7887 (m-40) outliers start: 5 outliers final: 4 residues processed: 50 average time/residue: 0.1500 time to fit residues: 13.0897 Evaluate side-chains 53 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 180 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 24 optimal weight: 2.9990 chunk 142 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** 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 = 0.3514 r_free = 0.3514 target = 0.094066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.074353 restraints weight = 67507.379| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 3.32 r_work: 0.3034 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11978 Z= 0.127 Angle : 0.427 5.076 16340 Z= 0.222 Chirality : 0.043 0.374 1917 Planarity : 0.003 0.038 2069 Dihedral : 5.055 59.968 2034 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.34 % Allowed : 10.48 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.23), residues: 1496 helix: 1.71 (0.22), residues: 620 sheet: -1.71 (0.33), residues: 248 loop : -1.46 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.010 0.001 TYR C 77 PHE 0.007 0.001 PHE A 296 TRP 0.011 0.001 TRP B 323 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00288 (11954) covalent geometry : angle 0.41254 (16272) SS BOND : bond 0.00090 ( 4) SS BOND : angle 0.43349 ( 8) hydrogen bonds : bond 0.03129 ( 500) hydrogen bonds : angle 3.81576 ( 1482) link_BETA1-4 : bond 0.00373 ( 12) link_BETA1-4 : angle 1.67403 ( 36) link_NAG-ASN : bond 0.00347 ( 8) link_NAG-ASN : angle 2.10167 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 53 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 170 ASN cc_start: 0.8356 (m-40) cc_final: 0.8073 (m-40) REVERT: D 170 ASN cc_start: 0.8213 (m-40) cc_final: 0.7880 (m-40) outliers start: 4 outliers final: 1 residues processed: 50 average time/residue: 0.1509 time to fit residues: 12.8548 Evaluate side-chains 50 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 109 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 10 optimal weight: 0.0030 chunk 57 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 112 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 100 optimal weight: 0.6980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 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 = 0.3534 r_free = 0.3534 target = 0.095454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.075316 restraints weight = 67064.402| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.35 r_work: 0.3047 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11978 Z= 0.090 Angle : 0.403 5.019 16340 Z= 0.211 Chirality : 0.042 0.377 1917 Planarity : 0.003 0.037 2069 Dihedral : 4.673 57.828 2034 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.09 % Allowed : 10.82 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.23), residues: 1496 helix: 1.85 (0.22), residues: 620 sheet: -1.60 (0.33), residues: 248 loop : -1.34 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 190 TYR 0.008 0.001 TYR D 286 PHE 0.005 0.001 PHE A 109 TRP 0.010 0.001 TRP C 323 HIS 0.002 0.000 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00202 (11954) covalent geometry : angle 0.39071 (16272) SS BOND : bond 0.00125 ( 4) SS BOND : angle 0.42132 ( 8) hydrogen bonds : bond 0.02911 ( 500) hydrogen bonds : angle 3.70388 ( 1482) link_BETA1-4 : bond 0.00391 ( 12) link_BETA1-4 : angle 1.50485 ( 36) link_NAG-ASN : bond 0.00258 ( 8) link_NAG-ASN : angle 1.95606 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 38 is missing expected H atoms. Skipping. Residue THR 44 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LEU 143 is missing expected H atoms. Skipping. Residue THR 145 is missing expected H atoms. Skipping. Residue SER 152 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue ILE 209 is missing expected H atoms. Skipping. Residue THR 210 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 234 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 200 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 352 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 80 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LYS 132 is missing expected H atoms. Skipping. Residue LYS 156 is missing expected H atoms. Skipping. Residue LYS 157 is missing expected H atoms. Skipping. Residue LYS 172 is missing expected H atoms. Skipping. Residue LYS 173 is missing expected H atoms. Skipping. Residue LYS 187 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LYS 268 is missing expected H atoms. Skipping. Residue LYS 279 is missing expected H atoms. Skipping. Residue LYS 301 is missing expected H atoms. Skipping. Residue LYS 334 is missing expected H atoms. Skipping. Residue LYS 346 is missing expected H atoms. Skipping. Residue LYS 364 is missing expected H atoms. Skipping. Residue LYS 370 is missing expected H atoms. Skipping. Residue LYS 379 is missing expected H atoms. Skipping. Residue VAL 382 is missing expected H atoms. Skipping. Residue THR 383 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8234 (m-30) cc_final: 0.7764 (p0) REVERT: B 170 ASN cc_start: 0.8338 (m-40) cc_final: 0.8043 (m-40) REVERT: D 170 ASN cc_start: 0.8205 (m-40) cc_final: 0.7863 (m-40) outliers start: 1 outliers final: 1 residues processed: 52 average time/residue: 0.1573 time to fit residues: 14.1643 Evaluate side-chains 51 residues out of total 1300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 50 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 141 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 77 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 10 ASN ** 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 = 0.3521 r_free = 0.3521 target = 0.094636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.074478 restraints weight = 67382.421| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.34 r_work: 0.3033 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11978 Z= 0.116 Angle : 0.413 4.915 16340 Z= 0.216 Chirality : 0.042 0.375 1917 Planarity : 0.003 0.038 2069 Dihedral : 4.573 55.322 2034 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.09 % Allowed : 10.48 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.23), residues: 1496 helix: 1.84 (0.22), residues: 620 sheet: -1.54 (0.34), residues: 248 loop : -1.29 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 190 TYR 0.009 0.001 TYR C 77 PHE 0.006 0.001 PHE A 296 TRP 0.010 0.001 TRP D 323 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00264 (11954) covalent geometry : angle 0.39999 (16272) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.41238 ( 8) hydrogen bonds : bond 0.03007 ( 500) hydrogen bonds : angle 3.70823 ( 1482) link_BETA1-4 : bond 0.00371 ( 12) link_BETA1-4 : angle 1.53573 ( 36) link_NAG-ASN : bond 0.00305 ( 8) link_NAG-ASN : angle 1.97311 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4139.19 seconds wall clock time: 71 minutes 11.22 seconds (4271.22 seconds total)