Starting phenix.real_space_refine on Sun Aug 24 12:53:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b69_44250/08_2025/9b69_44250.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b69_44250/08_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_44250/08_2025/9b69_44250.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b69_44250/08_2025/9b69_44250.map" model { file = "/net/cci-nas-00/data/ceres_data/9b69_44250/08_2025/9b69_44250.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b69_44250/08_2025/9b69_44250.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 11, 'GLU:plan': 9, 'GLN:plan1': 6, '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, 'ARG:plan': 10, 'ASP:plan': 6, 'GLU:plan': 13, 'ASN:plan1': 1} 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: {'ARG:plan': 8, 'GLU:plan': 10, 'ASN:plan1': 1, 'GLN:plan1': 3} 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: {'GLU:plan': 9, 'ARG:plan': 4, 'ASP:plan': 2, 'HIS:plan': 1, 'GLN:plan1': 1} 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: 2.17, per 1000 atoms: 0.19 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: 1.39 Conformation dependent library (CDL) restraints added in 690.9 milliseconds Enol-peptide restraints added in 1.7 microseconds 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: 0.46 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: 2.09 Time building geometry restraints manager: 1.74 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: 4.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.200 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- 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 : 5.61 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG A 198 TYR 0.011 0.001 TYR A 77 PHE 0.010 0.001 PHE D 181 TRP 0.015 0.001 TRP D 262 HIS 0.004 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00270 (11617) covalent geometry : angle 0.49186 (15853) SS BOND : bond 0.00203 ( 4) SS BOND : angle 1.11974 ( 8) hydrogen bonds : bond 0.12875 ( 543) hydrogen bonds : angle 5.89314 ( 1587) link_BETA1-4 : bond 0.00534 ( 6) link_BETA1-4 : angle 1.97747 ( 18) link_NAG-ASN : bond 0.00080 ( 5) link_NAG-ASN : angle 1.64994 ( 15) *********************** 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 : 0.395 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: 0.1435 time to fit residues: 27.8738 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 : 0.453 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 GLN B 207 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.129658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.099767 restraints weight = 18354.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.099147 restraints weight = 14159.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.100152 restraints weight = 16154.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.100773 restraints weight = 11604.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.101382 restraints weight = 10551.936| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 11632 Z= 0.335 Angle : 0.639 6.175 15894 Z= 0.334 Chirality : 0.046 0.160 1856 Planarity : 0.004 0.046 2040 Dihedral : 8.816 62.217 1834 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.37 % Allowed : 18.12 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.22), residues: 1488 helix: 1.46 (0.21), residues: 604 sheet: -1.34 (0.32), residues: 260 loop : -0.65 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 198 TYR 0.025 0.002 TYR C 77 PHE 0.016 0.002 PHE D 133 TRP 0.019 0.002 TRP C 323 HIS 0.007 0.002 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00796 (11617) covalent geometry : angle 0.62910 (15853) SS BOND : bond 0.00381 ( 4) SS BOND : angle 1.36422 ( 8) hydrogen bonds : bond 0.04384 ( 543) hydrogen bonds : angle 4.97366 ( 1587) link_BETA1-4 : bond 0.00832 ( 6) link_BETA1-4 : angle 2.66200 ( 18) link_NAG-ASN : bond 0.00649 ( 5) link_NAG-ASN : angle 2.16615 ( 15) *********************** 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 193 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8737 (mt) REVERT: C 180 LEU cc_start: 0.7859 (OUTLIER) cc_final: 0.7509 (tp) REVERT: C 280 TYR cc_start: 0.7061 (p90) cc_final: 0.6670 (p90) REVERT: C 339 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7145 (tm-30) REVERT: C 359 ASN cc_start: 0.8431 (t0) cc_final: 0.8216 (m-40) REVERT: A 202 ASN cc_start: 0.7707 (m110) cc_final: 0.7102 (t0) REVERT: D 318 ASN cc_start: 0.7906 (p0) cc_final: 0.7655 (p0) REVERT: D 380 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7903 (tpp) outliers start: 38 outliers final: 20 residues processed: 182 average time/residue: 0.1238 time to fit residues: 31.5157 Evaluate side-chains 163 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 321 VAL 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 41 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 66 optimal weight: 0.0060 chunk 81 optimal weight: 0.8980 chunk 109 optimal weight: 0.0270 chunk 107 optimal weight: 0.9980 overall best weight: 0.5454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 214 HIS 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 = 0.3684 r_free = 0.3684 target = 0.134329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103860 restraints weight = 18036.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105204 restraints weight = 13097.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.105999 restraints weight = 11472.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106526 restraints weight = 9756.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107107 restraints weight = 8863.059| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11632 Z= 0.097 Angle : 0.472 7.059 15894 Z= 0.245 Chirality : 0.041 0.146 1856 Planarity : 0.003 0.038 2040 Dihedral : 6.718 59.682 1826 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.22 % Allowed : 18.56 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.22), residues: 1488 helix: 1.85 (0.21), residues: 608 sheet: -1.22 (0.32), residues: 252 loop : -0.58 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 198 TYR 0.013 0.001 TYR A 127 PHE 0.009 0.001 PHE D 76 TRP 0.017 0.001 TRP D 262 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00215 (11617) covalent geometry : angle 0.46118 (15853) SS BOND : bond 0.00249 ( 4) SS BOND : angle 1.13963 ( 8) hydrogen bonds : bond 0.03175 ( 543) hydrogen bonds : angle 4.39557 ( 1587) link_BETA1-4 : bond 0.00723 ( 6) link_BETA1-4 : angle 2.49682 ( 18) link_NAG-ASN : bond 0.00076 ( 5) link_NAG-ASN : angle 1.88756 ( 15) *********************** 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 180 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8679 (mt) REVERT: C 339 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7297 (tm-30) REVERT: A 71 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6336 (m-10) REVERT: A 202 ASN cc_start: 0.7427 (m110) cc_final: 0.7084 (t0) REVERT: A 380 MET cc_start: 0.6293 (ttp) cc_final: 0.5973 (ttp) REVERT: B 68 ARG cc_start: 0.7503 (ttp-170) cc_final: 0.7298 (ttp-170) REVERT: B 259 ILE cc_start: 0.7936 (mt) cc_final: 0.7685 (mm) REVERT: D 318 ASN cc_start: 0.7897 (p0) cc_final: 0.7641 (p0) outliers start: 25 outliers final: 13 residues processed: 174 average time/residue: 0.1311 time to fit residues: 31.6294 Evaluate side-chains 158 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 266 GLU Chi-restraints excluded: chain A residue 321 VAL 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 7 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 45 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 131 optimal weight: 0.4980 chunk 113 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN B 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.102389 restraints weight = 18298.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103008 restraints weight = 14717.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.104237 restraints weight = 12857.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104647 restraints weight = 10097.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105287 restraints weight = 9670.764| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 11632 Z= 0.198 Angle : 0.519 5.203 15894 Z= 0.270 Chirality : 0.042 0.147 1856 Planarity : 0.003 0.038 2040 Dihedral : 6.273 57.915 1826 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.55 % Allowed : 18.65 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.22), residues: 1488 helix: 1.66 (0.21), residues: 612 sheet: -1.50 (0.31), residues: 268 loop : -0.49 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 198 TYR 0.017 0.002 TYR A 128 PHE 0.014 0.001 PHE B 258 TRP 0.015 0.001 TRP D 262 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00465 (11617) covalent geometry : angle 0.50751 (15853) SS BOND : bond 0.00285 ( 4) SS BOND : angle 1.10643 ( 8) hydrogen bonds : bond 0.03566 ( 543) hydrogen bonds : angle 4.49705 ( 1587) link_BETA1-4 : bond 0.00526 ( 6) link_BETA1-4 : angle 2.54462 ( 18) link_NAG-ASN : bond 0.00345 ( 5) link_NAG-ASN : angle 2.08677 ( 15) *********************** 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 189 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8719 (mt) REVERT: C 339 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7238 (tm-30) REVERT: A 190 ARG cc_start: 0.6855 (mmm-85) cc_final: 0.6246 (mmm-85) REVERT: A 202 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.7142 (t0) REVERT: A 380 MET cc_start: 0.6292 (ttp) cc_final: 0.5892 (ttp) REVERT: B 71 TYR cc_start: 0.7899 (m-80) cc_final: 0.7674 (m-10) REVERT: B 274 HIS cc_start: 0.5297 (OUTLIER) cc_final: 0.3505 (t70) REVERT: B 380 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7726 (ttt) REVERT: D 318 ASN cc_start: 0.7972 (p0) cc_final: 0.7750 (p0) outliers start: 40 outliers final: 29 residues processed: 177 average time/residue: 0.1305 time to fit residues: 31.7669 Evaluate side-chains 176 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.449 ------------------------------------------------------------------------------- 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 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 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 152 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 111 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 chunk 103 optimal weight: 0.3980 chunk 84 optimal weight: 4.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.131367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101718 restraints weight = 18211.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.102262 restraints weight = 14074.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.103257 restraints weight = 12740.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103794 restraints weight = 10198.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104421 restraints weight = 9662.328| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11632 Z= 0.178 Angle : 0.508 5.508 15894 Z= 0.265 Chirality : 0.042 0.161 1856 Planarity : 0.003 0.036 2040 Dihedral : 6.239 59.215 1826 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.80 % Allowed : 18.56 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.25 (0.22), residues: 1488 helix: 1.66 (0.21), residues: 612 sheet: -1.25 (0.32), residues: 252 loop : -0.66 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 198 TYR 0.015 0.001 TYR A 128 PHE 0.012 0.001 PHE B 258 TRP 0.015 0.001 TRP D 262 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00419 (11617) covalent geometry : angle 0.49672 (15853) SS BOND : bond 0.00324 ( 4) SS BOND : angle 1.69758 ( 8) hydrogen bonds : bond 0.03419 ( 543) hydrogen bonds : angle 4.45050 ( 1587) link_BETA1-4 : bond 0.00585 ( 6) link_BETA1-4 : angle 2.38208 ( 18) link_NAG-ASN : bond 0.00290 ( 5) link_NAG-ASN : angle 2.06849 ( 15) *********************** 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 208 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 154 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: C 14 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7960 (pp) REVERT: C 143 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8684 (mt) REVERT: C 339 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7264 (tm-30) REVERT: A 47 ILE cc_start: 0.8992 (mm) cc_final: 0.8585 (pt) REVERT: A 50 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6187 (pp) REVERT: A 71 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.5927 (m-10) REVERT: A 380 MET cc_start: 0.6273 (ttp) cc_final: 0.5773 (ttp) REVERT: B 68 ARG cc_start: 0.7417 (ttp-170) cc_final: 0.7207 (ttp-170) REVERT: B 71 TYR cc_start: 0.7850 (m-80) cc_final: 0.7598 (m-10) REVERT: B 189 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7553 (tp30) REVERT: B 274 HIS cc_start: 0.5405 (OUTLIER) cc_final: 0.3581 (t70) REVERT: B 380 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7792 (ttt) REVERT: D 304 ILE cc_start: 0.8636 (mm) cc_final: 0.8358 (mt) REVERT: D 318 ASN cc_start: 0.8009 (p0) cc_final: 0.7750 (p0) outliers start: 54 outliers final: 33 residues processed: 195 average time/residue: 0.1284 time to fit residues: 34.7544 Evaluate side-chains 182 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ILE 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 168 ILE 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 71 TYR 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 160 VAL 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 274 HIS Chi-restraints excluded: chain B residue 278 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 64 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 95 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.134497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.105165 restraints weight = 18135.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105647 restraints weight = 12900.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106761 restraints weight = 11925.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.107293 restraints weight = 9542.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107739 restraints weight = 9147.238| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1752 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= 0.099 Angle : 0.468 6.328 15894 Z= 0.244 Chirality : 0.040 0.153 1856 Planarity : 0.003 0.034 2040 Dihedral : 5.909 57.814 1826 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.46 % Allowed : 19.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (0.22), residues: 1488 helix: 1.85 (0.21), residues: 616 sheet: -1.16 (0.32), residues: 252 loop : -0.57 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 198 TYR 0.010 0.001 TYR A 77 PHE 0.010 0.001 PHE D 76 TRP 0.016 0.001 TRP D 262 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00227 (11617) covalent geometry : angle 0.45704 (15853) SS BOND : bond 0.00269 ( 4) SS BOND : angle 1.89730 ( 8) hydrogen bonds : bond 0.02945 ( 543) hydrogen bonds : angle 4.19800 ( 1587) link_BETA1-4 : bond 0.00748 ( 6) link_BETA1-4 : angle 2.18601 ( 18) link_NAG-ASN : bond 0.00088 ( 5) link_NAG-ASN : angle 1.89551 ( 15) *********************** 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 195 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8600 (mt) REVERT: A 47 ILE cc_start: 0.8973 (mm) cc_final: 0.8536 (pt) REVERT: A 190 ARG cc_start: 0.6795 (mmm-85) cc_final: 0.6054 (mmm-85) REVERT: B 71 TYR cc_start: 0.7848 (m-80) cc_final: 0.7624 (m-10) REVERT: B 274 HIS cc_start: 0.5272 (OUTLIER) cc_final: 0.3508 (t70) REVERT: D 304 ILE cc_start: 0.8611 (mm) cc_final: 0.8336 (mt) outliers start: 39 outliers final: 28 residues processed: 185 average time/residue: 0.1269 time to fit residues: 32.7559 Evaluate side-chains 169 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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 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 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 235 ILE Chi-restraints excluded: chain D residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 58 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 46 optimal weight: 0.0570 chunk 102 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 0.0970 chunk 75 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 120 optimal weight: 0.0060 chunk 54 optimal weight: 4.9990 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 HIS A 350 ASN B 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.135560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106619 restraints weight = 18121.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.107826 restraints weight = 13576.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108785 restraints weight = 11740.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109262 restraints weight = 9564.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109877 restraints weight = 9141.024| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11632 Z= 0.091 Angle : 0.463 7.405 15894 Z= 0.241 Chirality : 0.040 0.154 1856 Planarity : 0.003 0.031 2040 Dihedral : 5.725 59.047 1826 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.02 % Allowed : 20.52 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.22), residues: 1488 helix: 1.92 (0.22), residues: 616 sheet: -1.08 (0.32), residues: 252 loop : -0.52 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 300 TYR 0.010 0.001 TYR A 77 PHE 0.020 0.001 PHE A 181 TRP 0.015 0.001 TRP D 262 HIS 0.010 0.001 HIS B 46 Details of bonding type rmsd covalent geometry : bond 0.00209 (11617) covalent geometry : angle 0.45365 (15853) SS BOND : bond 0.00282 ( 4) SS BOND : angle 1.43510 ( 8) hydrogen bonds : bond 0.02851 ( 543) hydrogen bonds : angle 4.12775 ( 1587) link_BETA1-4 : bond 0.00644 ( 6) link_BETA1-4 : angle 2.09913 ( 18) link_NAG-ASN : bond 0.00115 ( 5) link_NAG-ASN : angle 1.78594 ( 15) *********************** 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 184 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8539 (mt) REVERT: A 47 ILE cc_start: 0.8955 (mm) cc_final: 0.8472 (pt) REVERT: A 279 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7490 (mtmt) REVERT: A 380 MET cc_start: 0.6175 (ttp) cc_final: 0.5846 (ttp) REVERT: B 68 ARG cc_start: 0.7176 (ttp-170) cc_final: 0.6843 (ttp-110) REVERT: B 71 TYR cc_start: 0.7832 (m-80) cc_final: 0.7621 (m-10) REVERT: B 274 HIS cc_start: 0.5134 (OUTLIER) cc_final: 0.3425 (t70) REVERT: D 304 ILE cc_start: 0.8602 (mm) cc_final: 0.8304 (mt) outliers start: 34 outliers final: 28 residues processed: 175 average time/residue: 0.1326 time to fit residues: 31.9098 Evaluate side-chains 172 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 235 ILE 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 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 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 78 optimal weight: 0.6980 chunk 135 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 146 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 B 219 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.132963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103947 restraints weight = 18131.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104565 restraints weight = 13967.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.105699 restraints weight = 12180.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.106325 restraints weight = 9829.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.106921 restraints weight = 9335.406| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11632 Z= 0.155 Angle : 0.495 6.591 15894 Z= 0.259 Chirality : 0.041 0.161 1856 Planarity : 0.003 0.035 2040 Dihedral : 5.765 57.053 1826 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.64 % Allowed : 20.25 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.22), residues: 1488 helix: 1.83 (0.22), residues: 616 sheet: -1.05 (0.33), residues: 252 loop : -0.57 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 198 TYR 0.013 0.001 TYR A 77 PHE 0.012 0.001 PHE B 258 TRP 0.014 0.001 TRP D 262 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00366 (11617) covalent geometry : angle 0.48580 (15853) SS BOND : bond 0.00248 ( 4) SS BOND : angle 1.54831 ( 8) hydrogen bonds : bond 0.03228 ( 543) hydrogen bonds : angle 4.30339 ( 1587) link_BETA1-4 : bond 0.00536 ( 6) link_BETA1-4 : angle 2.16580 ( 18) link_NAG-ASN : bond 0.00283 ( 5) link_NAG-ASN : angle 1.88170 ( 15) *********************** 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: 41 poor density : 152 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8618 (mt) REVERT: A 47 ILE cc_start: 0.8988 (mm) cc_final: 0.8504 (pt) REVERT: A 214 HIS cc_start: 0.6642 (OUTLIER) cc_final: 0.6163 (p90) REVERT: A 279 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7494 (mtmt) REVERT: A 361 MET cc_start: 0.6263 (ptp) cc_final: 0.5755 (ptp) REVERT: A 380 MET cc_start: 0.6261 (ttp) cc_final: 0.5948 (ttp) REVERT: B 71 TYR cc_start: 0.7893 (m-80) cc_final: 0.7663 (m-10) REVERT: B 274 HIS cc_start: 0.5132 (OUTLIER) cc_final: 0.3314 (t-170) REVERT: D 304 ILE cc_start: 0.8631 (mm) cc_final: 0.8343 (mt) outliers start: 41 outliers final: 28 residues processed: 183 average time/residue: 0.1314 time to fit residues: 33.3281 Evaluate side-chains 179 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 376 GLU 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 214 HIS 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 104 optimal weight: 30.0000 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.133041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.103933 restraints weight = 18135.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.104676 restraints weight = 14058.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105716 restraints weight = 12223.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.106458 restraints weight = 9884.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107026 restraints weight = 9188.498| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.1976 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= 0.146 Angle : 0.502 6.644 15894 Z= 0.262 Chirality : 0.041 0.159 1856 Planarity : 0.003 0.038 2040 Dihedral : 5.755 57.703 1826 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.55 % Allowed : 20.60 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.22), residues: 1488 helix: 1.77 (0.21), residues: 616 sheet: -1.05 (0.33), residues: 252 loop : -0.57 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 198 TYR 0.013 0.001 TYR A 77 PHE 0.010 0.001 PHE B 258 TRP 0.014 0.001 TRP D 262 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00345 (11617) covalent geometry : angle 0.49313 (15853) SS BOND : bond 0.00260 ( 4) SS BOND : angle 1.47975 ( 8) hydrogen bonds : bond 0.03203 ( 543) hydrogen bonds : angle 4.33129 ( 1587) link_BETA1-4 : bond 0.00583 ( 6) link_BETA1-4 : angle 2.12087 ( 18) link_NAG-ASN : bond 0.00218 ( 5) link_NAG-ASN : angle 1.88700 ( 15) *********************** 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 187 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8630 (mt) REVERT: A 25 GLU cc_start: 0.7251 (mm-30) cc_final: 0.7038 (mm-30) REVERT: A 47 ILE cc_start: 0.8983 (mm) cc_final: 0.8507 (pt) REVERT: A 190 ARG cc_start: 0.7066 (tpp80) cc_final: 0.6656 (mmm-85) REVERT: A 214 HIS cc_start: 0.6530 (OUTLIER) cc_final: 0.5863 (p90) REVERT: A 279 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7484 (mtmt) REVERT: A 361 MET cc_start: 0.6257 (ptp) cc_final: 0.5731 (ptp) REVERT: A 380 MET cc_start: 0.6259 (ttp) cc_final: 0.5947 (ttp) REVERT: B 68 ARG cc_start: 0.7309 (ttp-170) cc_final: 0.6788 (ttp-110) REVERT: B 71 TYR cc_start: 0.7887 (m-80) cc_final: 0.7632 (m-10) REVERT: B 274 HIS cc_start: 0.5137 (OUTLIER) cc_final: 0.3315 (t-170) REVERT: D 304 ILE cc_start: 0.8642 (mm) cc_final: 0.8355 (mt) outliers start: 40 outliers final: 33 residues processed: 178 average time/residue: 0.1339 time to fit residues: 32.7625 Evaluate side-chains 183 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 208 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 ASP 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 97 ILE Chi-restraints excluded: chain A residue 214 HIS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 0.1980 chunk 63 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 142 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 B 147 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.104697 restraints weight = 18101.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105059 restraints weight = 12845.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106334 restraints weight = 11666.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106734 restraints weight = 9366.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.107281 restraints weight = 9117.010| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1993 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= 0.110 Angle : 0.492 7.471 15894 Z= 0.255 Chirality : 0.041 0.159 1856 Planarity : 0.003 0.038 2040 Dihedral : 5.628 57.238 1826 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.20 % Allowed : 20.96 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.22), residues: 1488 helix: 1.83 (0.21), residues: 616 sheet: -1.02 (0.33), residues: 252 loop : -0.54 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 300 TYR 0.011 0.001 TYR A 77 PHE 0.009 0.001 PHE D 76 TRP 0.014 0.001 TRP D 262 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00257 (11617) covalent geometry : angle 0.48313 (15853) SS BOND : bond 0.00240 ( 4) SS BOND : angle 1.37403 ( 8) hydrogen bonds : bond 0.03040 ( 543) hydrogen bonds : angle 4.26955 ( 1587) link_BETA1-4 : bond 0.00576 ( 6) link_BETA1-4 : angle 2.06067 ( 18) link_NAG-ASN : bond 0.00132 ( 5) link_NAG-ASN : angle 1.82054 ( 15) ********************** 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 183 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: C 143 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8601 (mt) REVERT: A 25 GLU cc_start: 0.7182 (mm-30) cc_final: 0.6979 (mm-30) REVERT: A 47 ILE cc_start: 0.8985 (mm) cc_final: 0.8501 (pt) REVERT: A 190 ARG cc_start: 0.7020 (tpp80) cc_final: 0.6717 (mmm-85) REVERT: A 279 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7466 (mtmt) REVERT: A 361 MET cc_start: 0.6244 (ptp) cc_final: 0.5729 (ptp) REVERT: A 380 MET cc_start: 0.6225 (ttp) cc_final: 0.5898 (ttp) REVERT: B 68 ARG cc_start: 0.7312 (ttp-170) cc_final: 0.6788 (ttp-110) REVERT: B 71 TYR cc_start: 0.7863 (m-80) cc_final: 0.7635 (m-10) REVERT: B 274 HIS cc_start: 0.5156 (OUTLIER) cc_final: 0.3327 (t-170) REVERT: B 380 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7818 (ttp) REVERT: D 304 ILE cc_start: 0.8627 (mm) cc_final: 0.8345 (mt) outliers start: 36 outliers final: 32 residues processed: 174 average time/residue: 0.1326 time to fit residues: 31.8701 Evaluate side-chains 178 residues out of total 1292 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 208 VAL Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 252 ASP 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 234 LYS Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 249 ASP 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 274 HIS Chi-restraints excluded: chain B residue 278 ILE 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 145 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 55 optimal weight: 0.4980 chunk 59 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 8 optimal weight: 0.0970 chunk 67 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 126 optimal weight: 6.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.133197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.104196 restraints weight = 18282.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104648 restraints weight = 14155.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.105978 restraints weight = 12404.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.106497 restraints weight = 9692.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.107120 restraints weight = 9332.170| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11632 Z= 0.134 Angle : 0.496 6.564 15894 Z= 0.258 Chirality : 0.041 0.158 1856 Planarity : 0.003 0.038 2040 Dihedral : 5.582 57.008 1826 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.55 % Allowed : 20.87 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.22), residues: 1488 helix: 1.80 (0.21), residues: 616 sheet: -1.03 (0.33), residues: 252 loop : -0.56 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 300 TYR 0.012 0.001 TYR A 77 PHE 0.010 0.001 PHE B 258 TRP 0.013 0.001 TRP D 262 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd covalent geometry : bond 0.00315 (11617) covalent geometry : angle 0.48719 (15853) SS BOND : bond 0.00245 ( 4) SS BOND : angle 1.41852 ( 8) hydrogen bonds : bond 0.03141 ( 543) hydrogen bonds : angle 4.29255 ( 1587) link_BETA1-4 : bond 0.00574 ( 6) link_BETA1-4 : angle 2.11480 ( 18) link_NAG-ASN : bond 0.00207 ( 5) link_NAG-ASN : angle 1.82753 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1909.94 seconds wall clock time: 33 minutes 55.76 seconds (2035.76 seconds total)