Starting phenix.real_space_refine on Tue May 20 13:02:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b69_44250/05_2025/9b69_44250.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b69_44250/05_2025/9b69_44250.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b69_44250/05_2025/9b69_44250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b69_44250/05_2025/9b69_44250.map" model { file = "/net/cci-nas-00/data/ceres_data/9b69_44250/05_2025/9b69_44250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b69_44250/05_2025/9b69_44250.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 10695 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 7264 2.51 5 N 1875 2.21 5 O 2195 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11370 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2763 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 219 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 9, 'ARG:plan': 11, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 118 Chain: "A" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2774 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 245 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 13, 'ARG:plan': 10, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 2814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2814 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 146 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 10, 'ARG:plan': 8, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 95 Chain: "D" Number of atoms: 2871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2871 Classifications: {'peptide': 374} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 363} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'HIS:plan': 1, 'ARG:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 71 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: 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.90, per 1000 atoms: 0.61 Number of scatterers: 11370 At special positions: 0 Unit cell: (145.14, 123.82, 94.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2195 8.00 N 1875 7.00 C 7264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 315 " distance=2.03 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 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 G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG B 901 " - " ASN B 355 " " NAG E 1 " - " ASN C 241 " " NAG F 1 " - " ASN A 241 " " NAG G 1 " - " ASN B 241 " " NAG H 1 " - " ASN D 241 " Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.6 seconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2768 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 41.6% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'C' and resid 23 through 36 Processing helix chain 'C' and resid 54 through 69 Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.885A pdb=" N ILE C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 143 through 157 Processing helix chain 'C' and resid 172 through 187 removed outlier: 4.045A pdb=" N LYS C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 252 through 265 removed outlier: 3.551A pdb=" N ARG C 261 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 302 Processing helix chain 'C' and resid 324 through 334 removed outlier: 4.083A pdb=" N GLU C 328 " --> pdb=" O GLY C 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 37 Processing helix chain 'A' and resid 54 through 69 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 157 Processing helix chain 'A' and resid 174 through 187 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 252 through 264 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 323 through 334 removed outlier: 3.789A 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 69 Processing helix chain 'B' and resid 81 through 93 removed outlier: 3.611A pdb=" N ILE B 85 " --> pdb=" O SER B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 129 Processing helix chain 'B' and resid 143 through 157 Processing helix chain 'B' and resid 169 through 173 removed outlier: 3.540A pdb=" N LYS B 172 " --> pdb=" O ASN B 169 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS B 173 " --> pdb=" O ASN B 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 169 through 173' Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 232 through 237 removed outlier: 4.394A pdb=" N PHE B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 263 Processing helix chain 'B' and resid 279 through 301 Processing helix chain 'B' and resid 325 through 334 removed outlier: 3.732A pdb=" N ILE B 329 " --> pdb=" O GLN B 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 36 Processing helix chain 'D' and resid 54 through 68 Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.742A pdb=" N ILE D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 143 through 157 Processing helix chain 'D' and resid 172 through 187 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 231 through 235 removed outlier: 4.050A pdb=" N LYS D 234 " --> pdb=" O ASP D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 4.095A pdb=" N THR D 264 " --> pdb=" O GLU D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 303 Processing helix chain 'D' and resid 325 through 335 Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 50 removed outlier: 6.612A pdb=" N ILE C 12 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N HIS C 46 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE C 14 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ASP C 48 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N GLY C 16 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU C 50 " --> pdb=" O GLY C 16 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N PHE C 18 " --> pdb=" O LEU C 50 " (cutoff:3.500A) removed outlier: 10.065A pdb=" N ALA C 72 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLN C 13 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N PHE C 74 " --> pdb=" O GLN C 13 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLY C 15 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE C 73 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE C 96 " --> pdb=" O ILE C 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 159 through 164 removed outlier: 7.414A pdb=" N LYS C 132 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N ILE C 193 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ALA C 134 " --> pdb=" O ILE C 193 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ASP C 195 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU C 136 " --> pdb=" O ASP C 195 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE C 245 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL C 242 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLU C 362 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LYS C 370 " --> pdb=" O GLU C 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 337 through 340 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 49 removed outlier: 7.229A pdb=" N ILE A 14 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ASP A 48 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY A 16 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N GLN A 13 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N PHE A 74 " --> pdb=" O GLN A 13 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N GLY A 15 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 73 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE A 96 " --> pdb=" O ILE A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 161 through 164 removed outlier: 6.451A pdb=" N ALA A 134 " --> pdb=" O ILE A 193 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ASP A 195 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LEU A 136 " --> pdb=" O ASP A 195 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 245 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N VAL A 242 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU A 362 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LYS A 370 " --> pdb=" O GLU A 362 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS A 364 " --> pdb=" O PRO A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 337 through 340 removed outlier: 3.617A pdb=" N LYS A 346 " --> pdb=" O ILE A 354 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 42 through 47 removed outlier: 6.764A pdb=" N ILE B 12 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N HIS B 46 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ILE B 14 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA B 72 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE B 73 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N PHE B 96 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 159 through 164 removed outlier: 4.988A pdb=" N ARG B 191 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR B 220 " --> pdb=" O SER B 243 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N PHE B 245 " --> pdb=" O TYR B 220 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ILE B 222 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL B 242 " --> pdb=" O LEU B 363 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ILE B 358 " --> pdb=" O TYR B 373 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR B 373 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ILE B 360 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 362 " --> pdb=" O ARG B 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 337 through 340 Processing sheet with id=AB1, first strand: chain 'D' and resid 43 through 49 removed outlier: 6.365A pdb=" N ILE D 12 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N HIS D 46 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ILE D 14 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ASP D 48 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY D 16 " --> pdb=" O ASP D 48 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA D 72 " --> pdb=" O GLN D 13 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 73 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 159 through 164 removed outlier: 7.450A pdb=" N PHE D 133 " --> pdb=" O THR D 161 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ILE D 163 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR D 135 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG D 191 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR D 220 " --> pdb=" O SER D 243 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N PHE D 245 " --> pdb=" O TYR D 220 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE D 222 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N VAL D 242 " --> pdb=" O LEU D 363 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU D 362 " --> pdb=" O LYS D 370 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS D 370 " --> pdb=" O GLU D 362 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LYS D 364 " --> pdb=" O PRO D 368 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 337 through 339 543 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.11 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3711 1.34 - 1.46: 2734 1.46 - 1.58: 5116 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 11617 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" C1 BMA G 3 " pdb=" C2 BMA G 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.37e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.05e+00 ... (remaining 11612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 15634 1.77 - 3.54: 181 3.54 - 5.30: 29 5.30 - 7.07: 8 7.07 - 8.84: 1 Bond angle restraints: 15853 Sorted by residual: angle pdb=" CA LYS D 187 " pdb=" CB LYS D 187 " pdb=" CG LYS D 187 " ideal model delta sigma weight residual 114.10 120.29 -6.19 2.00e+00 2.50e-01 9.58e+00 angle pdb=" CB LYS D 187 " pdb=" CG LYS D 187 " pdb=" CD LYS D 187 " ideal model delta sigma weight residual 111.30 118.17 -6.87 2.30e+00 1.89e-01 8.93e+00 angle pdb=" C LEU D 186 " pdb=" N LYS D 187 " pdb=" CA LYS D 187 " ideal model delta sigma weight residual 122.31 116.56 5.75 2.00e+00 2.50e-01 8.27e+00 angle pdb=" N LYS D 187 " pdb=" CA LYS D 187 " pdb=" CB LYS D 187 " ideal model delta sigma weight residual 110.46 114.67 -4.21 1.54e+00 4.22e-01 7.46e+00 angle pdb=" CA LEU C 233 " pdb=" CB LEU C 233 " pdb=" CG LEU C 233 " ideal model delta sigma weight residual 116.30 125.14 -8.84 3.50e+00 8.16e-02 6.38e+00 ... (remaining 15848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 6298 21.82 - 43.65: 462 43.65 - 65.47: 74 65.47 - 87.29: 25 87.29 - 109.11: 8 Dihedral angle restraints: 6867 sinusoidal: 2543 harmonic: 4324 Sorted by residual: dihedral pdb=" CB CYS C 63 " pdb=" SG CYS C 63 " pdb=" SG CYS C 315 " pdb=" CB CYS C 315 " ideal model delta sinusoidal sigma weight residual -86.00 -48.10 -37.90 1 1.00e+01 1.00e-02 2.02e+01 dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual 288.71 179.60 109.11 1 3.00e+01 1.11e-03 1.42e+01 dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.62 108.33 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 6864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1596 0.055 - 0.111: 223 0.111 - 0.166: 33 0.166 - 0.221: 2 0.221 - 0.276: 2 Chirality restraints: 1856 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA LYS D 187 " pdb=" N LYS D 187 " pdb=" C LYS D 187 " pdb=" CB LYS D 187 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.66e-01 ... (remaining 1853 not shown) Planarity restraints: 2045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 98 " 0.025 5.00e-02 4.00e+02 3.71e-02 2.20e+00 pdb=" N PRO D 99 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 98 " -0.023 5.00e-02 4.00e+02 3.47e-02 1.93e+00 pdb=" N PRO C 99 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 98 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 99 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 99 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 99 " 0.016 5.00e-02 4.00e+02 ... (remaining 2042 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 455 2.72 - 3.27: 11559 3.27 - 3.81: 19355 3.81 - 4.36: 22231 4.36 - 4.90: 39070 Nonbonded interactions: 92670 Sorted by model distance: nonbonded pdb=" OE1 GLU A 25 " pdb=" OG SER A 282 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASP C 116 " pdb=" OH TYR C 356 " model vdw 2.201 3.040 nonbonded pdb=" OH TYR D 135 " pdb=" OD2 ASP D 195 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR B 71 " pdb=" O ILE B 306 " model vdw 2.229 3.040 nonbonded pdb=" OH TYR D 128 " pdb=" OE2 GLU D 362 " model vdw 2.247 3.040 ... (remaining 92665 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 43 or (resid 44 and (name N or name CA or name \ C or name O or name CB )) or resid 45 through 53 or (resid 54 and (name N or nam \ e CA or name C or name O or name CB )) or resid 55 through 78 or (resid 79 throu \ gh 80 and (name N or name CA or name C or name O or name CB )) or resid 81 throu \ gh 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 through 155 or (resid 156 through 157 and (name N or name CA or name \ C or name O or name CB )) or resid 158 through 183 or (resid 184 through 190 and \ (name N or name CA or name C or name O or name CB )) or resid 191 through 199 o \ r (resid 200 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 01 through 230 or (resid 231 through 232 and (name N or name CA or name C or nam \ e O or name CB )) or resid 233 or (resid 234 through 236 and (name N or name CA \ or name C or name O or name CB )) or resid 237 through 256 or (resid 257 and (na \ me N or name CA or name C or name O or name CB )) or resid 258 through 265 or (r \ esid 266 through 269 and (name N or name CA or name C or name O or name CB )) or \ resid 270 through 273 or (resid 274 and (name N or name CA or name C or name O \ or name CB )) or resid 275 through 278 or (resid 279 and (name N or name CA or n \ ame C or name O or name CB )) or resid 280 through 296 or (resid 297 and (name N \ or name CA or name C or name O or name CB )) or resid 298 through 301 or (resid \ 302 through 303 and (name N or name CA or name C or name O or name CB )) or res \ id 304 through 333 or (resid 334 through 335 and (name N or name CA or name C or \ name O or name CB )) or resid 336 through 345 or (resid 346 and (name N or name \ CA or name C or name O or name CB )) or resid 347 through 351 or (resid 352 and \ (name N or name CA or name C or name O or name CB )) or resid 353 through 383)) \ selection = (chain 'B' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 22 or (resid 23 and (name N or nam \ e CA or name C or name O or name CB )) or resid 24 through 43 or (resid 44 and ( \ name N or name CA or name C or name O or name CB )) or resid 45 through 47 or (r \ esid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thr \ ough 103 or (resid 104 and (name N or name CA or name C or name O or name CB )) \ or resid 105 through 115 or (resid 116 and (name N or name CA or name C or name \ O or name CB )) or resid 117 through 139 or (resid 140 and (name N or name CA or \ name C or name O or name CB )) or resid 141 through 155 or (resid 156 through 1 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 158 through \ 169 or (resid 170 and (name N or name CA or name C or name O or name CB )) or r \ esid 171 through 177 or (resid 178 and (name N or name CA or name C or name O or \ name CB )) or resid 179 through 183 or (resid 184 through 190 and (name N or na \ me CA or name C or name O or name CB )) or resid 191 through 199 or (resid 200 a \ nd (name N or name CA or name C or name O or name CB )) or resid 201 through 205 \ or (resid 206 and (name N or name CA or name C or name O or name CB )) or resid \ 207 through 212 or (resid 213 and (name N or name CA or name C or name O or nam \ e CB )) or resid 214 through 215 or (resid 216 and (name N or name CA or name C \ or name O or name CB )) or resid 217 through 230 or (resid 231 through 232 and ( \ name N or name CA or name C or name O or name CB )) or resid 233 or (resid 234 t \ hrough 236 and (name N or name CA or name C or name O or name CB )) or resid 237 \ through 273 or (resid 274 and (name N or name CA or name C or name O or name CB \ )) or resid 275 through 278 or (resid 279 and (name N or name CA or name C or n \ ame O or name CB )) or resid 280 through 293 or (resid 294 through 295 and (name \ N or name CA or name C or name O or name CB )) or resid 296 through 298 or (res \ id 299 through 303 and (name N or name CA or name C or name O or name CB )) or r \ esid 304 through 305 or (resid 306 and (name N or name CA or name C or name O or \ name CB )) or resid 307 through 333 or (resid 334 through 335 and (name N or na \ me CA or name C or name O or name CB )) or resid 336 through 361 or (resid 362 a \ nd (name N or name CA or name C or name O or name CB )) or resid 363 through 368 \ or (resid 369 through 370 and (name N or name CA or name C or name O or name CB \ )) or resid 371 through 383)) selection = (chain 'C' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 22 or (resid 23 and (name N or nam \ e CA or name C or name O or name CB )) or resid 24 through 36 or (resid 37 and ( \ name N or name CA or name C or name O or name CB )) or resid 38 through 47 or (r \ esid 48 and (name N or name CA or name C or name O or name CB )) or resid 49 thr \ ough 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) or \ resid 55 through 103 or (resid 104 and (name N or name CA or name C or name O o \ r name CB )) or resid 105 through 115 or (resid 116 and (name N or name CA or na \ me C or name O or name CB )) or resid 117 through 139 or (resid 140 and (name N \ or name CA or name C or name O or name CB )) or resid 141 through 169 or (resid \ 170 and (name N or name CA or name C or name O or name CB )) or resid 171 throug \ h 184 or (resid 185 through 190 and (name N or name CA or name C or name O or na \ me CB )) or resid 191 through 205 or (resid 206 and (name N or name CA or name C \ or name O or name CB )) or resid 207 through 212 or (resid 213 and (name N or n \ ame CA or name C or name O or name CB )) or resid 214 through 215 or (resid 216 \ and (name N or name CA or name C or name O or name CB )) or resid 217 through 26 \ 5 or (resid 266 through 269 and (name N or name CA or name C or name O or name C \ B )) or resid 270 through 273 or (resid 274 and (name N or name CA or name C or \ name O or name CB )) or resid 275 through 293 or (resid 294 through 295 and (nam \ e N or name CA or name C or name O or name CB )) or resid 296 or (resid 297 and \ (name N or name CA or name C or name O or name CB )) or resid 298 or (resid 299 \ through 303 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 4 through 305 or (resid 306 and (name N or name CA or name C or name O or name C \ B )) or resid 307 through 351 or (resid 352 and (name N or name CA or name C or \ name O or name CB )) or resid 353 through 383)) selection = (chain 'D' and (resid 10 through 12 or (resid 13 and (name N or name CA or name \ C or name O or name CB )) or resid 14 through 19 or (resid 20 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 21 through 23 and (name N or na \ me CA or name C or name O or name CB )) or resid 24 through 36 or (resid 37 and \ (name N or name CA or name C or name O or name CB )) or resid 38 through 43 or ( \ resid 44 and (name N or name CA or name C or name O or name CB )) or resid 45 th \ rough 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) o \ r resid 55 through 79 or (resid 80 and (name N or name CA or name C or name O or \ name CB )) or resid 81 through 115 or (resid 116 and (name N or name CA or name \ C or name O or name CB )) or resid 117 or (resid 118 and (name N or name CA or \ name C or name O or name CB )) or resid 119 through 139 or (resid 140 and (name \ N or name CA or name C or name O or name CB )) or resid 141 through 155 or (resi \ d 156 through 157 and (name N or name CA or name C or name O or name CB )) or re \ sid 158 through 169 or (resid 170 and (name N or name CA or name C or name O or \ name CB )) or resid 171 through 172 or (resid 173 and (name N or name CA or name \ C or name O or name CB )) or resid 174 through 177 or (resid 178 and (name N or \ name CA or name C or name O or name CB )) or resid 179 through 181 or (resid 18 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 183 or (resi \ d 184 through 190 and (name N or name CA or name C or name O or name CB )) or re \ sid 191 through 196 or (resid 197 and (name N or name CA or name C or name O or \ name CB )) or resid 198 through 199 or (resid 200 and (name N or name CA or name \ C or name O or name CB )) or resid 201 through 205 or (resid 206 and (name N or \ name CA or name C or name O or name CB )) or resid 207 through 212 or (resid 21 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 214 through \ 215 or (resid 216 and (name N or name CA or name C or name O or name CB )) or re \ sid 217 through 230 or (resid 231 through 232 and (name N or name CA or name C o \ r name O or name CB )) or resid 233 or (resid 234 through 236 and (name N or nam \ e CA or name C or name O or name CB )) or resid 237 through 260 or (resid 261 an \ d (name N or name CA or name C or name O or name CB )) or resid 262 through 265 \ or (resid 266 through 269 and (name N or name CA or name C or name O or name CB \ )) or resid 270 through 278 or (resid 279 and (name N or name CA or name C or na \ me O or name CB )) or resid 280 through 296 or (resid 297 and (name N or name CA \ or name C or name O or name CB )) or resid 298 or (resid 299 through 303 and (n \ ame N or name CA or name C or name O or name CB )) or resid 304 through 305 or ( \ resid 306 and (name N or name CA or name C or name O or name CB )) or resid 307 \ or (resid 308 through 309 and (name N or name CA or name C or name O or name CB \ )) or resid 310 through 324 or (resid 325 and (name N or name CA or name C or na \ me O or name CB )) or resid 326 through 330 or (resid 331 through 332 and (name \ N or name CA or name C or name O or name CB )) or resid 333 or (resid 334 throug \ h 335 and (name N or name CA or name C or name O or name CB )) or resid 336 thro \ ugh 345 or (resid 346 and (name N or name CA or name C or name O or name CB )) o \ r resid 347 through 351 or (resid 352 and (name N or name CA or name C or name O \ or name CB )) or resid 353 through 361 or (resid 362 and (name N or name CA or \ name C or name O or name CB )) or resid 363 through 369 or (resid 370 and (name \ N or name CA or name C or name O or name CB )) or resid 371 through 383)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.150 Find NCS groups from input model: 0.540 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11632 Z= 0.128 Angle : 0.499 8.841 15894 Z= 0.256 Chirality : 0.041 0.276 1856 Planarity : 0.003 0.037 2040 Dihedral : 16.281 109.115 4087 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.36 % Allowed : 20.34 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.23), residues: 1488 helix: 2.10 (0.22), residues: 604 sheet: -0.99 (0.33), residues: 252 loop : -0.42 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.004 0.001 HIS A 46 PHE 0.010 0.001 PHE D 181 TYR 0.011 0.001 TYR A 77 ARG 0.007 0.001 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 5) link_NAG-ASN : angle 1.64994 ( 15) link_BETA1-4 : bond 0.00534 ( 6) link_BETA1-4 : angle 1.97747 ( 18) hydrogen bonds : bond 0.12875 ( 543) hydrogen bonds : angle 5.89314 ( 1587) SS BOND : bond 0.00203 ( 4) SS BOND : angle 1.11974 ( 8) covalent geometry : bond 0.00270 (11617) covalent geometry : angle 0.49186 (15853) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 140 time to evaluate : 1.227 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8844 (mm) cc_final: 0.8546 (mt) outliers start: 4 outliers final: 3 residues processed: 143 average time/residue: 0.2826 time to fit residues: 54.7404 Evaluate side-chains 141 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 138 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain D residue 13 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 GLN A 24 GLN B 207 GLN D 107 HIS D 170 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099637 restraints weight = 18119.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098491 restraints weight = 15115.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099395 restraints weight = 13986.569| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 11632 Z= 0.285 Angle : 0.616 6.343 15894 Z= 0.319 Chirality : 0.045 0.159 1856 Planarity : 0.004 0.043 2040 Dihedral : 8.583 59.510 1834 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.55 % Allowed : 18.03 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1488 helix: 1.39 (0.21), residues: 612 sheet: -1.38 (0.32), residues: 260 loop : -0.61 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 323 HIS 0.007 0.002 HIS D 93 PHE 0.014 0.002 PHE D 76 TYR 0.022 0.002 TYR C 77 ARG 0.007 0.001 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 5) link_NAG-ASN : angle 2.13418 ( 15) link_BETA1-4 : bond 0.00634 ( 6) link_BETA1-4 : angle 2.77211 ( 18) hydrogen bonds : bond 0.04306 ( 543) hydrogen bonds : angle 4.91452 ( 1587) SS BOND : bond 0.00363 ( 4) SS BOND : angle 1.40321 ( 8) covalent geometry : bond 0.00667 (11617) covalent geometry : angle 0.60490 (15853) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8746 (mt) REVERT: C 180 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7449 (tp) REVERT: C 267 GLU cc_start: 0.8004 (tp30) cc_final: 0.7631 (tp30) REVERT: C 280 TYR cc_start: 0.7050 (p90) cc_final: 0.6703 (p90) REVERT: C 323 TRP cc_start: 0.7645 (OUTLIER) cc_final: 0.7442 (p-90) REVERT: C 339 GLU cc_start: 0.7483 (tm-30) cc_final: 0.7215 (tm-30) REVERT: C 359 ASN cc_start: 0.8375 (t0) cc_final: 0.8129 (m-40) REVERT: A 202 ASN cc_start: 0.7687 (m110) cc_final: 0.7078 (t0) REVERT: D 318 ASN cc_start: 0.7944 (p0) cc_final: 0.7711 (p0) REVERT: D 344 ASN cc_start: 0.7990 (t0) cc_final: 0.7777 (t0) REVERT: D 380 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7945 (tpp) outliers start: 40 outliers final: 22 residues processed: 185 average time/residue: 0.2451 time to fit residues: 62.9550 Evaluate side-chains 168 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 323 TRP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 362 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 380 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 60 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 140 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS A 290 GLN B 112 GLN D 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.133689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.103363 restraints weight = 18243.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.104285 restraints weight = 13286.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105324 restraints weight = 11925.853| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11632 Z= 0.108 Angle : 0.473 6.893 15894 Z= 0.246 Chirality : 0.040 0.142 1856 Planarity : 0.003 0.038 2040 Dihedral : 6.691 59.570 1826 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.40 % Allowed : 18.47 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.22), residues: 1488 helix: 1.80 (0.21), residues: 608 sheet: -1.22 (0.32), residues: 252 loop : -0.60 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 262 HIS 0.005 0.001 HIS A 214 PHE 0.008 0.001 PHE D 133 TYR 0.017 0.001 TYR A 127 ARG 0.008 0.000 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00093 ( 5) link_NAG-ASN : angle 1.85849 ( 15) link_BETA1-4 : bond 0.00685 ( 6) link_BETA1-4 : angle 2.52537 ( 18) hydrogen bonds : bond 0.03235 ( 543) hydrogen bonds : angle 4.43205 ( 1587) SS BOND : bond 0.00260 ( 4) SS BOND : angle 1.16271 ( 8) covalent geometry : bond 0.00244 (11617) covalent geometry : angle 0.46132 (15853) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.487 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8701 (mt) REVERT: C 339 GLU cc_start: 0.7521 (tm-30) cc_final: 0.7317 (tm-30) REVERT: C 359 ASN cc_start: 0.8253 (t0) cc_final: 0.8036 (m-40) REVERT: A 71 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6356 (m-10) REVERT: A 190 ARG cc_start: 0.7018 (tpp80) cc_final: 0.6783 (mmm-85) REVERT: A 202 ASN cc_start: 0.7456 (m110) cc_final: 0.7089 (t0) REVERT: B 68 ARG cc_start: 0.7493 (ttp-170) cc_final: 0.7282 (ttp-170) REVERT: B 259 ILE cc_start: 0.7950 (mt) cc_final: 0.7699 (mm) REVERT: D 318 ASN cc_start: 0.7915 (p0) cc_final: 0.7659 (p0) outliers start: 27 outliers final: 15 residues processed: 175 average time/residue: 0.2570 time to fit residues: 62.3943 Evaluate side-chains 160 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 71 TYR Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 123 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 142 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 107 optimal weight: 0.3980 chunk 38 optimal weight: 8.9990 chunk 144 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.134466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104458 restraints weight = 17997.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106102 restraints weight = 13216.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.106906 restraints weight = 11333.403| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11632 Z= 0.103 Angle : 0.451 5.709 15894 Z= 0.235 Chirality : 0.040 0.136 1856 Planarity : 0.003 0.033 2040 Dihedral : 5.880 56.518 1826 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.29 % Allowed : 18.56 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.22), residues: 1488 helix: 1.90 (0.21), residues: 612 sheet: -1.20 (0.32), residues: 252 loop : -0.53 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 262 HIS 0.006 0.001 HIS D 46 PHE 0.012 0.001 PHE B 56 TYR 0.015 0.001 TYR A 128 ARG 0.006 0.000 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 5) link_NAG-ASN : angle 1.86638 ( 15) link_BETA1-4 : bond 0.00634 ( 6) link_BETA1-4 : angle 2.37580 ( 18) hydrogen bonds : bond 0.03011 ( 543) hydrogen bonds : angle 4.24921 ( 1587) SS BOND : bond 0.00218 ( 4) SS BOND : angle 0.95033 ( 8) covalent geometry : bond 0.00237 (11617) covalent geometry : angle 0.43973 (15853) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 1.247 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8648 (mt) REVERT: C 180 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7474 (tp) REVERT: A 190 ARG cc_start: 0.6978 (tpp80) cc_final: 0.6756 (mmm160) REVERT: A 202 ASN cc_start: 0.7270 (OUTLIER) cc_final: 0.6990 (t0) REVERT: A 380 MET cc_start: 0.6142 (ttp) cc_final: 0.5888 (ttp) REVERT: B 274 HIS cc_start: 0.5194 (OUTLIER) cc_final: 0.3529 (t70) REVERT: B 380 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7679 (ttt) REVERT: D 318 ASN cc_start: 0.7899 (p0) cc_final: 0.7668 (p0) outliers start: 37 outliers final: 27 residues processed: 178 average time/residue: 0.2574 time to fit residues: 63.7557 Evaluate side-chains 174 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 142 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 202 ASN Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 262 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 14 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 127 optimal weight: 0.2980 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 112 GLN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.102994 restraints weight = 18067.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103717 restraints weight = 14503.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105013 restraints weight = 12456.936| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 11632 Z= 0.193 Angle : 0.515 6.673 15894 Z= 0.269 Chirality : 0.042 0.165 1856 Planarity : 0.003 0.037 2040 Dihedral : 6.065 58.116 1826 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.26 % Allowed : 18.47 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.22), residues: 1488 helix: 1.73 (0.21), residues: 612 sheet: -1.46 (0.31), residues: 268 loop : -0.48 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.006 0.001 HIS D 46 PHE 0.026 0.001 PHE A 181 TYR 0.015 0.002 TYR C 77 ARG 0.007 0.001 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00360 ( 5) link_NAG-ASN : angle 2.03804 ( 15) link_BETA1-4 : bond 0.00538 ( 6) link_BETA1-4 : angle 2.38647 ( 18) hydrogen bonds : bond 0.03532 ( 543) hydrogen bonds : angle 4.44215 ( 1587) SS BOND : bond 0.00317 ( 4) SS BOND : angle 1.62711 ( 8) covalent geometry : bond 0.00454 (11617) covalent geometry : angle 0.50437 (15853) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8667 (mt) REVERT: C 188 LYS cc_start: 0.3442 (tttm) cc_final: 0.3197 (tttp) REVERT: A 47 ILE cc_start: 0.9017 (mm) cc_final: 0.8619 (pt) REVERT: A 50 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6253 (pp) REVERT: A 380 MET cc_start: 0.6241 (ttp) cc_final: 0.5843 (ttp) REVERT: B 68 ARG cc_start: 0.7437 (ttp-170) cc_final: 0.7236 (ttp-170) REVERT: B 274 HIS cc_start: 0.5325 (OUTLIER) cc_final: 0.3496 (t70) REVERT: B 380 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7771 (ttp) REVERT: D 304 ILE cc_start: 0.8636 (mm) cc_final: 0.8354 (mt) REVERT: D 318 ASN cc_start: 0.7959 (p0) cc_final: 0.7696 (p0) outliers start: 48 outliers final: 32 residues processed: 191 average time/residue: 0.2629 time to fit residues: 69.5580 Evaluate side-chains 179 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 282 SER Chi-restraints excluded: chain D residue 361 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 9 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 131 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 92 optimal weight: 0.0070 chunk 64 optimal weight: 5.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105475 restraints weight = 18032.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.105777 restraints weight = 12816.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106794 restraints weight = 11948.619| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11632 Z= 0.098 Angle : 0.469 6.477 15894 Z= 0.243 Chirality : 0.040 0.160 1856 Planarity : 0.003 0.035 2040 Dihedral : 5.752 57.554 1826 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.02 % Allowed : 19.72 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.22), residues: 1488 helix: 1.90 (0.22), residues: 616 sheet: -1.15 (0.32), residues: 252 loop : -0.53 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 262 HIS 0.006 0.001 HIS D 46 PHE 0.010 0.001 PHE D 76 TYR 0.011 0.001 TYR A 128 ARG 0.008 0.001 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00061 ( 5) link_NAG-ASN : angle 1.89068 ( 15) link_BETA1-4 : bond 0.00659 ( 6) link_BETA1-4 : angle 2.14970 ( 18) hydrogen bonds : bond 0.02898 ( 543) hydrogen bonds : angle 4.18236 ( 1587) SS BOND : bond 0.00221 ( 4) SS BOND : angle 1.70888 ( 8) covalent geometry : bond 0.00227 (11617) covalent geometry : angle 0.45893 (15853) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8619 (mt) REVERT: A 380 MET cc_start: 0.6160 (ttp) cc_final: 0.5799 (ttp) REVERT: B 274 HIS cc_start: 0.5280 (OUTLIER) cc_final: 0.3511 (t70) REVERT: D 304 ILE cc_start: 0.8608 (mm) cc_final: 0.8331 (mt) outliers start: 34 outliers final: 24 residues processed: 182 average time/residue: 0.2558 time to fit residues: 64.8792 Evaluate side-chains 173 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 282 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 123 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 76 optimal weight: 0.0470 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 25 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 overall best weight: 0.7494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 214 HIS A 350 ASN B 207 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106176 restraints weight = 18196.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106141 restraints weight = 14348.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107153 restraints weight = 14486.475| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11632 Z= 0.098 Angle : 0.456 6.712 15894 Z= 0.237 Chirality : 0.040 0.154 1856 Planarity : 0.003 0.031 2040 Dihedral : 5.607 55.907 1826 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.11 % Allowed : 19.98 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1488 helix: 1.97 (0.22), residues: 616 sheet: -1.07 (0.32), residues: 252 loop : -0.50 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.010 0.001 HIS B 46 PHE 0.009 0.001 PHE D 56 TYR 0.010 0.001 TYR A 77 ARG 0.008 0.001 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00084 ( 5) link_NAG-ASN : angle 1.77386 ( 15) link_BETA1-4 : bond 0.00576 ( 6) link_BETA1-4 : angle 2.11817 ( 18) hydrogen bonds : bond 0.02917 ( 543) hydrogen bonds : angle 4.10471 ( 1587) SS BOND : bond 0.00215 ( 4) SS BOND : angle 1.50665 ( 8) covalent geometry : bond 0.00225 (11617) covalent geometry : angle 0.44666 (15853) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8599 (mt) REVERT: A 47 ILE cc_start: 0.8909 (mm) cc_final: 0.8423 (pt) REVERT: A 380 MET cc_start: 0.6164 (ttp) cc_final: 0.5719 (ttp) REVERT: B 68 ARG cc_start: 0.7190 (ttp-170) cc_final: 0.6872 (ttp-110) REVERT: B 274 HIS cc_start: 0.5168 (OUTLIER) cc_final: 0.3422 (t70) REVERT: B 380 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7763 (ttp) REVERT: D 304 ILE cc_start: 0.8610 (mm) cc_final: 0.8310 (mt) outliers start: 35 outliers final: 28 residues processed: 175 average time/residue: 0.2968 time to fit residues: 72.7170 Evaluate side-chains 177 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 262 TRP Chi-restraints excluded: chain D residue 282 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 141 optimal weight: 30.0000 chunk 8 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 136 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.106964 restraints weight = 18108.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.107239 restraints weight = 14101.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108310 restraints weight = 14357.714| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11632 Z= 0.099 Angle : 0.463 7.134 15894 Z= 0.242 Chirality : 0.040 0.153 1856 Planarity : 0.003 0.036 2040 Dihedral : 5.538 55.943 1826 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.29 % Allowed : 19.98 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.23), residues: 1488 helix: 2.01 (0.22), residues: 616 sheet: -1.00 (0.33), residues: 252 loop : -0.48 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.005 0.001 HIS D 46 PHE 0.008 0.001 PHE D 76 TYR 0.010 0.001 TYR A 77 ARG 0.008 0.001 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 5) link_NAG-ASN : angle 1.74572 ( 15) link_BETA1-4 : bond 0.00600 ( 6) link_BETA1-4 : angle 2.06504 ( 18) hydrogen bonds : bond 0.02857 ( 543) hydrogen bonds : angle 4.09418 ( 1587) SS BOND : bond 0.00210 ( 4) SS BOND : angle 1.34283 ( 8) covalent geometry : bond 0.00230 (11617) covalent geometry : angle 0.45430 (15853) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8585 (mt) REVERT: A 47 ILE cc_start: 0.8893 (mm) cc_final: 0.8372 (pt) REVERT: A 279 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7495 (mtmt) REVERT: B 274 HIS cc_start: 0.5145 (OUTLIER) cc_final: 0.3353 (t-170) REVERT: D 304 ILE cc_start: 0.8620 (mm) cc_final: 0.8318 (mt) outliers start: 37 outliers final: 31 residues processed: 184 average time/residue: 0.2543 time to fit residues: 64.8080 Evaluate side-chains 178 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 144 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 262 TRP Chi-restraints excluded: chain D residue 282 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 113 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 146 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 93 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 30 optimal weight: 0.0770 chunk 86 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106518 restraints weight = 18135.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106312 restraints weight = 15521.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107351 restraints weight = 16979.390| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11632 Z= 0.097 Angle : 0.465 7.008 15894 Z= 0.243 Chirality : 0.040 0.152 1856 Planarity : 0.003 0.039 2040 Dihedral : 5.492 55.767 1826 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.37 % Allowed : 20.25 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.23), residues: 1488 helix: 2.04 (0.22), residues: 616 sheet: -1.00 (0.33), residues: 252 loop : -0.47 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.006 0.001 HIS D 46 PHE 0.008 0.001 PHE D 76 TYR 0.010 0.001 TYR A 77 ARG 0.009 0.001 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 5) link_NAG-ASN : angle 1.69916 ( 15) link_BETA1-4 : bond 0.00579 ( 6) link_BETA1-4 : angle 2.01671 ( 18) hydrogen bonds : bond 0.02842 ( 543) hydrogen bonds : angle 4.11388 ( 1587) SS BOND : bond 0.00201 ( 4) SS BOND : angle 1.24680 ( 8) covalent geometry : bond 0.00227 (11617) covalent geometry : angle 0.45677 (15853) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8548 (mt) REVERT: A 47 ILE cc_start: 0.8907 (mm) cc_final: 0.8374 (pt) REVERT: A 279 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7473 (mtmt) REVERT: A 380 MET cc_start: 0.6142 (ttp) cc_final: 0.5814 (ttp) REVERT: B 68 ARG cc_start: 0.7278 (ttp-170) cc_final: 0.6803 (ttp-110) REVERT: B 274 HIS cc_start: 0.5209 (OUTLIER) cc_final: 0.3386 (t-170) REVERT: D 304 ILE cc_start: 0.8614 (mm) cc_final: 0.8315 (mt) outliers start: 38 outliers final: 32 residues processed: 172 average time/residue: 0.2574 time to fit residues: 61.2585 Evaluate side-chains 179 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 279 LYS Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 262 TRP Chi-restraints excluded: chain D residue 282 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 4 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 139 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 chunk 29 optimal weight: 0.0030 chunk 142 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106155 restraints weight = 18038.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107718 restraints weight = 12883.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108553 restraints weight = 11014.364| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11632 Z= 0.094 Angle : 0.469 7.351 15894 Z= 0.244 Chirality : 0.040 0.151 1856 Planarity : 0.003 0.038 2040 Dihedral : 5.390 55.444 1826 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.20 % Allowed : 20.43 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.23), residues: 1488 helix: 2.06 (0.22), residues: 616 sheet: -0.95 (0.33), residues: 252 loop : -0.44 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.007 0.001 HIS D 46 PHE 0.009 0.001 PHE D 76 TYR 0.011 0.001 TYR A 77 ARG 0.009 0.000 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 5) link_NAG-ASN : angle 1.61279 ( 15) link_BETA1-4 : bond 0.00551 ( 6) link_BETA1-4 : angle 1.94668 ( 18) hydrogen bonds : bond 0.02776 ( 543) hydrogen bonds : angle 4.06997 ( 1587) SS BOND : bond 0.00189 ( 4) SS BOND : angle 1.14394 ( 8) covalent geometry : bond 0.00218 (11617) covalent geometry : angle 0.46194 (15853) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8554 (mt) REVERT: C 213 LYS cc_start: 0.7935 (mttt) cc_final: 0.7684 (mptt) REVERT: A 47 ILE cc_start: 0.8896 (mm) cc_final: 0.8351 (pt) REVERT: A 339 GLU cc_start: 0.6684 (mp0) cc_final: 0.6365 (mp0) REVERT: A 361 MET cc_start: 0.6223 (ptp) cc_final: 0.5763 (ptp) REVERT: A 380 MET cc_start: 0.6195 (ttp) cc_final: 0.5879 (ttp) REVERT: B 68 ARG cc_start: 0.7235 (ttp-170) cc_final: 0.6769 (ttp-110) REVERT: B 274 HIS cc_start: 0.5161 (OUTLIER) cc_final: 0.3363 (t-170) REVERT: D 304 ILE cc_start: 0.8628 (mm) cc_final: 0.8334 (mt) outliers start: 36 outliers final: 31 residues processed: 176 average time/residue: 0.2557 time to fit residues: 62.7579 Evaluate side-chains 177 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 144 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 361 MET Chi-restraints excluded: chain C residue 376 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 95 SER Chi-restraints excluded: chain A residue 196 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 159 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 282 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain D residue 13 GLN Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 82 VAL Chi-restraints excluded: chain D residue 145 THR Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 262 TRP Chi-restraints excluded: chain D residue 282 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 66 optimal weight: 0.0570 chunk 72 optimal weight: 0.0970 chunk 97 optimal weight: 4.9990 chunk 62 optimal weight: 0.0070 chunk 113 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107544 restraints weight = 18065.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107740 restraints weight = 13923.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108783 restraints weight = 14066.856| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11632 Z= 0.089 Angle : 0.463 8.502 15894 Z= 0.241 Chirality : 0.040 0.149 1856 Planarity : 0.003 0.039 2040 Dihedral : 5.302 55.043 1826 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.93 % Allowed : 20.69 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.23), residues: 1488 helix: 2.09 (0.22), residues: 616 sheet: -0.88 (0.33), residues: 252 loop : -0.43 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 262 HIS 0.007 0.001 HIS D 46 PHE 0.016 0.001 PHE A 62 TYR 0.011 0.001 TYR A 77 ARG 0.009 0.000 ARG A 198 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 5) link_NAG-ASN : angle 1.55526 ( 15) link_BETA1-4 : bond 0.00565 ( 6) link_BETA1-4 : angle 1.89710 ( 18) hydrogen bonds : bond 0.02734 ( 543) hydrogen bonds : angle 4.03193 ( 1587) SS BOND : bond 0.00166 ( 4) SS BOND : angle 1.15287 ( 8) covalent geometry : bond 0.00206 (11617) covalent geometry : angle 0.45570 (15853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3316.22 seconds wall clock time: 58 minutes 57.76 seconds (3537.76 seconds total)